-
Notifications
You must be signed in to change notification settings - Fork 9
/
Copy pathRELEASE_NOTES.txt
3184 lines (2221 loc) · 128 KB
/
RELEASE_NOTES.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
RELEASE NOTES FOR SeqMonk v1.48.1
---------------------------------
1. Fixed a bug in the launch script which meant that memory
settings weren't detected correctly unless java was
installed on the system.
2. Made all preferences for the read count quantitation be
remembered between runs.
3. Removed spurious additional label in the BAM file import
options dialog.
4. Don't add projects which fail to load to the recently used
file list.
5. Update install instructions for M1 mac users.
RELEASE NOTES FOR SeqMonk v1.48.0
---------------------------------
A mix of bugfixes and some internal restructuring
1. Fixed the crash reporter which couldn't cope with https URLs
2. Changed the cache folder code to reduce the number of files
created in a single directory.
3. Added an option to the BAM file import to bring in data
which has barcodes or sample names embedded in the read IDs
4. Show the strand in the feature search results.
5. Vastly improve the speed of switching chromosomes or resizing
the chromosome view when lots of tracks are being displayed.
RELEASE NOTES FOR SeqMonk v1.47.2
---------------------------------
Many bugfixes...
1. Fix cache crash in seqmonk_import
2. Add java executable detection to seqmonk_import
3. Increase min R version to 4.0.3 because of bioconductor changes
4. Fix OSX launcher to work on older version of OSX
5. Allow 1-to-many comparisons in the DESeq filter
6. Fix stored filter preferences crash
7. Fix edge case mistake in feature filter overlaps
8. Automatically detect new OSX R Framework location
9. Update name cache when renaming features
RELEASE NOTES FOR SeqMonk v1.47.1
---------------------------------
This version contains some minor fixes.
Changes include:
1. Increased the minimum R version to 4.x.x. since R3.6 no longer
works for installing BioConductor packages.
2. Hopefully finally stop OSX from trying to compile R packages
from source when it doesn't need to.
3. Improve the efficiency of displaying annotation counts
4. Make genomes with annotation versions >99 sort correctly
5. Increase the number of allowed nodes in the probe list overlap
plot to 500
6. Add more options to the logistic regression filter
RELEASE NOTES FOR SeqMonk v1.47.0
---------------------------------
This version introduces some major changes for users of Mac OSX
and improves a lot of existing functionality.
There are two major changes of note:
1. The way the OSX package is built has been changed so that we can
deal with the new security model in OSX v10.15 (Catalina). People
working on that version will have found that they were unable to
load or save data to anywhere other than their home directory.
This new version now tests for limited disk access on OSX and if
it finds it it will point to instructions for how SeqMonk can be
given more generous permissions to read data from places like USB
drives, network shares and the Desktop.
2. We've made a relatively minor change to the way that RNA-Seq
quantitation works. When we merge transcript isoforms we used to
prefer matching transcripts based on them having compatible names
(eg ABC-201 would merge with ABC-202), *and* based on them actually
overlapping in the genome. We found though that some gene models
from Ensembl broke these assumptions (ie there are cases with
two different genes with identical names which overlap, and cases
of genes with multiple transcripts which don't overlap). These
cases are all nuts but they exist so we need to deal with them. We've
now changed to prefer using the "gene_id" annotation on transcripts
to decide which ones to merge, which deals better with these edge
cases. What this means though is that if you have an existing
RNA-Seq analysis in a project and you re-quantitate it having moved
to the new SeqMonk version that your probe set will be replaced as
it won't match the exsting set because of these changes. You will
therefore need to either re-create your filtered lists using the
new probe set - or stick to an older version of SeqMonk to finish
off those existing projects.
Other more minor changes are:
3. Improve the default matching options and save name for annotated
probe reports.
4. Added a vistory event for adding annotation
5. Added replicate set colouring to boxplots and beanplots
6. Made the default heatmap colours more friendly to colourblind people
7. Changed the min R version to 3.6 as Bioconductor is broken for
versions older than that.
8. Fixed a StarWars layout bug for multiple lists and one store.
9. Use https to communicate with web services
10. Try to improve R package installs on OSX
RELEASE NOTES FOR SeqMonk v1.46.0
---------------------------------
The v1.46.0 release introduces a couple of new features and fixes
some bugs.
The main changes are:
1. In statistical tests which can use more than 2 replicate sets
we now remember the order of selection of the sets in the options
so that the meaning of the fold change values is deterministic, ie
if you are comparing WT and KO you can choose to have the change as
either WT/KO or KO/WT in the report.
2. Fixed a bug where the intersect lists filter could make project files
which couldn't be re-loaded.
3. Added suitable track headers to make exported BED files more compatible
with UCSC browser
4. Allowed custom distances for "not close to" feature filter
5. Added an option to define co-factors when constructing a linear model
for DESeq2.
6. Fixed the save data option in the quantitation trend heatmap
7. Fixed PCA domain quantitation probe generation
8. Added the current quantitation values to the HiC report
9. Make the annotation set name the same as the feature name for imported
annotation.
10. Made the linux launch script SLURM aware so it configures memory limits
correctly.
11. Fix the warning of replacing probes in the RNA-Seq quantitation pipeline
so it only warns if it's actually going to replace them.
12. In DESeq2 pairwise comparisons we now report both the raw log2FoldChange
and the shrunken log2FoldChange.
RELEASE NOTES FOR SeqMonk v1.45.4
---------------------------------
This release is a bugfix release for the last version which resolves
an issue where small probes might not be drawn in the chromsome view
if their inferred size was less than 1 pixel.
It also introduces a copule of other minor changes:
1. Fix a probe drawing optimisation bug which caused some small probes
not to be drawn.
2. Add the option to highlight replicate sets in the line graph.
3. Annotate the variance filter results with the actual variance
values which were used for the test.
4. Improved the efficiency of drawing raw reads in the chromosome view
for replicate sets and data groups.
RELEASE NOTES FOR SeqMonk v1.45.3
---------------------------------
This release adds some useful functionality and cleans up a lot of
the new functions which have been added in recent releases. The main
changes are:
1. Indexed colours now duplicate if you're looking at expanded
replicate sets
2. Genome view block display now works
3. Added an option to apply the same manual correction to all samples
4. Added an option to make an annotation track instead of a probe set
for all probe generators
5. Allow probe sets to be called something other than "All Probes"
6. Allow annotated probe reports to be annotated with list values from
any combination of probe lists
7. Allow any images to be pasted into Vistories
8. Added a --introns option to the command line importer
9. Fixed per-probe normalisation when the "Use visible stores" option is
selected
10. Added the ability to label multiple points in all scatterplot type
displays
11. Added a new normalisation method based on subtracting a linear
trend from your data
12. Added a "sum" and "divide" option to to per-probe normalisation
13. Make seqmonk prompt on exit if a vistory has been modified and
viewed but not saved.
14. Allow all graphics exports to go straight to the clipboard
15. Created a vistory event for hierarchical cluster probe generation
RELEASE NOTES FOR SeqMonk v1.45.2
---------------------------------
This is a bugfix and stability release which tidies up a number of
areas. The main changes are:
1. Update vistory filter events to have the number of probes and
the name of the filter attached to them.
2. Fix a versioning bug when cross-importing annotation from another
project. Also allow cross importing between different annotation
versions of the same genome assembly.
3. Added a duplicate list filter which makes it easier to create
additional structure in a set of filtered probes.
4. Allow images to be moved up and down in vistories
5. Make the difference quantitation introduce NA values for ratio
measures when the total number of observations is very small.
6. Fix an updating bug when changing the number of pseudo chromosomes
when building a custom genome.
7. When auto-creating Data Groups only add each data set to one group.
8. Allow the creation of projects using just a control genome.
9. Add a save option to the probe list overlap matrix.
10. Improve the description of the percentile value filter.
11. Generate vistory events for probe lists created in plots
12. Add the replicate set name to the plot area in variation plots.
13. Fix the genome view image export to not include scroll bars.
RELEASE NOTES FOR SeqMonk v1.45.1
---------------------------------
This is a bugfix release which resolves some issues in the previous
release. It also adds some minor additional functionality.
Changes in this release are:
1. We fixed a bug in the packaging script for OSX which meant that
SeqMonk was not using the bundled JRE and was reliant on the
presence of a Java installation on the host machine. This also
caused a failure to launch on machines running a version of
Java older than 1.8.
2. We updated our BAM parser from the old samtools java library to
the newer htslib parser. This should resolve crashes caused when
the mapping command line recorded in the BAM header contained a
colon. Using the newer parser should also be somewhat quicker.
3. We fixed some limitations in Vistories. The table of contents
in the HTML report won't now truncate on smaller screens. We
capture some additional events which we were missing before.
Additional fixes will follow in future releases.
4. We fixed a crash in the List Annotation Value filter.
5. We added a new display option to change how replicate sets treat
probes which have quantitations for some (but not all) of their
members. Previously we had returned an NA value for the mean of
the probe if any member contained an NA. You can now choose to
return the mean of however many members contain valid values to
give more complete coverage of your data.
RELEASE NOTES FOR SeqMonk v1.45.0
---------------------------------
SeqMonk v1.45.0 is a major release which introduces some big changes
in the program.
The two major changes with this release are:
1. The introduction of Vistories, which are a way of documenting
your SeqMonk analysis. This is a document mixing the automatic
collection of events in the program with embedding graphics and
tables and allowing you to annotate the analysis with titles
and text. Vistories can be saved and loaded and can be exported
to HTML files for archiving and distribution.
2. With the change in licensing of the Oracle JRE we have made the
decision to stop relying on a JRE on the host computer and are
instead shipping embedded copies of the AdoptOpenJDK distributions
of java along with SeqMonk. This means that we now have platform
specific versions of SeqMonk for Windows, Linux and OSX, and that
the install procedure is much simpler than before since java is
no longer required to be separately installed.
In addition to these major features we have added a number of other
changes in this release.
- The LIMMA filter can now analyse multiple replicate sets in a single
operation.
- A bug in the Probe Trend plot when using the "scale within each
data store" option was fixed.
- We have removed the option to allow the storage of uncompressed
project files. In future all project files will be compressed.
- The list annotation filter can now use annotations coming from
lists other than the one you are filtering.
RELEASE NOTES FOR SeqMonk v1.44.0
---------------------------------
This release makes a major change in the way that probe lists annotations
are handled to make them much more flexible. It also introduces some
new filtering, visualisation and reporting options as well as fixing
a bug in the read position probe generator.
Major changes are:
- Probe lists can now record multiple named attributes (and can have
no attribute at all). This means that a statistical filter can now
record a p-value, q-value and fold change all together in the same
list for example.
- Added a probe list annotation value filter to allow for additional
filtering based on the contents of a probe lists annotations.
- Updated the DESeq and EdgeR, LIMMA, T-test/ANOVA, Intensity Diff
filters to record p-value,q-value and log2 fold change.
- Added a volcano plot to visualise hits for statistical search
result lists. Works for DESeq and EdgeR at the moment and will
support more tests in future.
- Added a custom layout for the chromosome view to more efficiently
handle the structure of the tracks, especially where there are
large numbers of tracks in a project.
- Added an option to do bulk renaming of data stores to the DataSet
editor
- Improved the layout of data tracks when there are a lot of them
- Added a track number to the data track selector
- Fixed a bug in the read position probe generator which meant that
reads on different strands were counted separately even if the
ignore strand option was selected
- Added fastseg to the R package requirements to make sure its there
for people using the segmentation tool
- Made changes to improve the speed of project saving
- Fixed a crash in the PCA plot when the data contains no variance
- Added an option to export annotation tracks as a BED file
- Added a match by name option to the feature report
- Added a generic NOT option to all feature filter matching types
- Updated the R installer code to respect a locally set preferred
CRAN repository, and to use the new BiocManager to install
bioconductor packages if appropriate.
RELEASE NOTES FOR SeqMonk v1.43.0
---------------------------------
This release adds some interesting new functionality for segregating
quantitation, and has some speed improvements as well as fixing some
bugs.
Main changes were:
- Fixed a bug which broke data imports in Bed and BedPE format
- Added drawing optimisation to the chromosome view to make it more
efficient displaying tracks with very high coverage
- Sped up the operation of DataGroups and ReplicateSets when collating
raw reads
- Added a new intersect lists filter to provide more filtering options
when combining lists together
- Changed the order of operations when saving files to reduce the
chances of data loss if something odd happens to the filesystem
whilst saving
- Improved the efficiency of the read position probe generator
- Added a segmentation filter to split quantitations into physically
connected groups
- Added the ability to cross import annotation tracks between projects
- Added an annotation editor to make it easy to rename or delete large
batches of annotation quickly
- Reduced the compression when saving to make it quicker
- Fixed a crash in the variance intensity difference filter if null
quantitations were present
RELEASE NOTES FOR SeqMonk v1.42.1
---------------------------------
This release was an opportunity for a general cleanup of a lot of cosmetic
issues which had been building up, as well as addressing a number of bugs.
Things which we fixed were:
- Fixed the text alignment on a lot of plot axes to be more pretty
- Fixed a data scaling bug on the QQ plot which sometimes missed out the
last point
- Fixed a crash in LIMMA when data contained NA values
- Fixed a cancellation bug in the HiC heatmap
- Fixed a null pointer bug in the proportion of library bug
- Added an option to save the data from the quantitation trend plot
- Added whitespace support to generic text import
- We now record the import options used when importing data
- Handle platforms where we can't automatically open a web browser better
- Fixed a bug where the read position probe generator only did a single chromosome
- Improved the layout of the quantitation trend heatmap
- Fixed a bug with NA or infinite values in the quantitation trend plot
RELEASE NOTES FOR SeqMonk v1.42.0
---------------------------------
This release has a fix for a potentially nasty data import bug introduced in
v1.40.1 and adds some new visualisation features.
#############################
# Important Data Import Bug #
#############################
We are indebted to John Chuang for spotting a data import bug which was
introduced in v1.40.1 and which could corrupt data imported from sorted
BAM files containing duplicated sequences. We'll do a full write up
elsewhere but the details of the bug can be seen in:
https://github.com/s-andrews/SeqMonk/issues/99
In short, if you have imported a sorted BAM file using SeqMonk v1.40.1 or
v1.41.0 then you may have had some duplicate reads silently discarded. The
issue could also theoretically affect sorted files, but the number of
sequences affected would be extremely low and is unlikely to materially
affect any datasets.
Projects which had data imported in an earlier version of seqmonk, and the
project was opened and saved in the affected versions are *not* affected.
The bug is in the import step.
If you imported sorted files into an affected version of the program then
we recommend that you create a new project and re-import the BAM files
using seqmonk v1.42.0 (or later).
Other changes in this release:
- Added a size factor normalisation quantitation
- Fixed a data update bug when creating custom genomes
- Added a new Quantitation Trend Heatmap plot, and optimised the old
Quantitation Trend Plot code
- Worked around an EdgeR installation bug which caused the EdgeR
filter to break.
- Fixed a problem with the linux themeing on Ubuntu 18.04
RELEASE NOTES FOR SeqMonk v1.41.0
---------------------------------
This release adds some new functionality, but also tidies up a lot of existing
features, making them work more smoothly.
- Added a QQ plot
- Improved the options and multiple testing correction in the logistic
regression filter.
- Fixed a slowness issue when working with hundreds of samples.
- Added a mechanism to allow projects to update to newer versions of
core annotations in the same assembly.
- Added a fix for the RNA-Seq QC plot when there isn't a rRNA track in
the annotation.
- Modified the DESeq filter to allow multiple group comparisons by using
the Likelihood ratio test.
- Report the parameters estimated by the RNA-Seq pipeline.
RELEASE NOTES FOR SeqMonk v1.40.1
---------------------------------
This is a bugfix release of seqmonk which adds some optimisations to the
background data model and fixes a number of bugs.
- Changed the internal data model to store positions and counts separately
to make the storage of heavily duplicated data much more efficient
- Added a LIMMA statistical filter
- Modified the GTF parser to better deal with the structure of Ensembl
GTF files.
- Changed all of the launchers so you can pass a file name to open. Allows
file extensions to be associated with seqmonk so you can open projects
by double clicking on them.
- Improve the merging of transcripts in the RNA-Seq pipeline to use
gene ids where they are present in the annotation so we don't get
spurious merging of overlapping transcripts on the same strand which
are annotated as belonging to different genes.
- Updated the genome processing scripts so that gene_ids are added to
all transcripts
- Fixed a crash in the aligned probes plot when no data stores are visible
- Fixed a display bug for the list of features in the feature filter and
quantitation trend plot.
- Fixed an inefficient packing algorithm when the number of reads was too
great to be displayed within the available height of the chromosome view.
RELEASE NOTES FOR SeqMonk v1.40.0
---------------------------------
This release does some major reorganisation of the filtering menu as well as
adding new functionality. Major changes are:
- Completely restructured the statistics filter menus so that they are
now arranged by the type of data they apply to.
- Added an option to detect and remove duplication in the RNA-Seq
quantitation pipeline.
- Added a new variant of the EdgeR filter which can work on for/rev
ratio data such as methylation data.
- Added an option to change the startup memory settings from the usual
preferences dialog.
- Added an R debug mode to make it easier to track down problems with R
based functionality.
- Fixed a bug in the variation plot for data containing NaN values
- Fixed a regression which meant some functionality didn't work on systems
running java 1.6
- Added an option to create data groups or replicate sets from pre-prepared
lists of data store names.
- Added a global correction to the aligned probes plot to make the plots
more directly comparable.
- Fixed a bug in the exporting of images from the aligned probes plot.
- Collated error messages to help interpreting large numbers of errors.
- Added a strand bias plot
RELEASE NOTES FOR SeqMonk v1.39.0
---------------------------------
This release is a mix of new features and bug and usability fixes for existing
features. Major changes are:
- Added the ability to have multiple annotation versions for the same genome
assembly release. We needed a way to update the annotations used for some of
the major eukaryotic genomes, when the sequence level assembly hadn't actually
changed. All genomes can now have multiple versions distinguished by the Ensembl
release number from which they came. The genome selection interface now shows
the different annotation versions for the same genome assembly grouped together.
- Added a parser for the BEDPE file format
- Added a better filtering for absolute change to the binomial, chi-square and
logistic regression filters.
- The hierarchical cluster plot now allows for the highlighting of replicate sets
at the top.
- The gene set filter now provides the option to use the Kolmogorov-Smirnov test
as well as the t-test when finding changing gene sets
- Altered the feature filter to allow it to simultaneously use multiple feature tracks
- Improved the scaling of the aligned probes plot so that the absolute numbers reported
are more meaningful
- Added a scale bar to the aligned probes plot
- Fixed a crash in the PCA plot when no data remained after removing null values
- Fixed a crash when saving results from the correlation matrix
- Fixed a bug which allowed replicate sets to be added to other replicate sets
when auto-creating sets in the data store tree
RELEASE NOTES FOR SeqMonk v1.38.2
---------------------------------
This is a bugfix release which mainly addresses a bug in the most recent
jave release on OSX. Specific changes in this release are:
- Fixed a hang bug specifically triggered in java v1.8_131 when creating
any report. The bug doesn't affect other platforms, or previous versions
of the JRE.
- Fixed a problem with the auto-setup of the perplexity setting in the Tsne
plot which affected projects with fewer than 7 samnples.
- Fixed a bug which caused the intensity gene set plot to not clean up
temporary probe lists when the list of hits was sorted.
RELEASE NOTES FOR SeqMonk v1.38.1
---------------------------------
This is a bugfix release which addresses some issues found in the previous
release. Specifically
- We fixed a performance bug when creating custom genomes from fasta or gff
files with very large numbers of sequences in them. This would have affected
people building custom genomes from very fragmented sets of contigs.
- We added a scale bar to the HiC heatmap
- We changed the TSNE code to use Rtnse instead of tsne to work round a bug and
to improve performance
- We added some more debugging output to the launch script to make it easier to
debug launching problems
- We fixed a bug in the SplicingEfficiency pipeline affecting genomes with
non-Ensembl naming schemes
- We fixed a bug in PCA plotting when showing labels in plots with overlapping
points
RELEASE NOTES FOR SeqMonk v1.38.0
---------------------------------
This release adds some new plotting options for data store similarity and
greatly improves the workflow for the analysis of splicing as well as
adding some more general bug fixes and improvements.
Major changes are:
- Added a TSNE plot for clustering data stores
- Added colouring to the correlation matrix
- Added a logistic regression splicing statistical filter
- Greatly improved the efficiency of the exactly overlap quantitation
- Added strand information to probe reports
- Fixed a bug in the launcher for UTF8 locales
- Fixed a bug in the normalisation of paired end RNA-Seq data
- Fixed a crash in bioconductor installation
RELEASE NOTES FOR SeqMonk v1.37.1
---------------------------------
This release is a minor bugfix release. Updating to this release is only
necessary for people directly affected by one of the bugs below:
- Fixed a bug in the reporting of R errors where the full R trace wasn't
attached to the crash report making it difficult to identify the cause
of R problems.
- Fixed a bug in the generation of custom genomes where feature names
containing a forward slash in their names would cause a failure of the
feature caching system.
- Fixed an out of date warning in the RNA-Seq pipeline which hadn't been
updated to the new option names in the BAM import dialog.
RELEASE NOTES FOR SeqMonk v1.37.0
---------------------------------
This release adds a lot of new and modified functionality to make the program
easier to use for some common tasks.
The changes in this release are:
- Added an option to the ChiSquare and Logistic Regression statistics to
resample the read ratios based on a current normalised percentage quantitation.
Provides lots of new possibilities for the analysis of BS-Seq data.
- Changed the heatmap view to use the currently set positive/negative scale
when performing euclidean clustering
- Fixed a bug in PCA plotting where NA or infinite quantitated values were
present
- Rewrote the features filter to make it much more powerful
- Fixed a bug in seqmonk_import if you specified a filename in the current
directory
- Updated seqmonk_import to allow the import of bismark coverage files
- Fixed error reporting in seqmonk_import
- Hugely optimised the exact overlap quantitation
- Made the status bar show the stand of any highlighted probe
- Allow the crash email to be changed from the preferences dialog
- Added more options to deduplication to account for different duplication types
- Stopped the RNA-Seq QC plot from duplicating prefixes when doing multiple filters
RELEASE NOTES FOR SeqMonk v1.36.0
---------------------------------
This release adds one new major piece of functionality to seqmonk and fixes a
bug in the bean plot.
The new functionality is a non-interactive import script 'seqmonk_import'. This
script allows you to create a new seqmonk project in a completely automated way
so that you don't need to launch an interactive session to do your initial data
import. This can be really useful where data might be stored on a cluster where
interactive sessions are impractical, and will save the hassle of having to
transfer all of the BAM files to a local machine to set up the project.
The bug fix affects the high end of the quantitation distribution in beanplots. In
some cases probes with counts in the highest bins were being counted multiple times
causing the top end of the plot to stretch in a way which didn't actually reflect the
distribution of the data. This issue is now fixed.
RELEASE NOTES FOR SeqMonk v1.35.0
---------------------------------
We're having our windows 10 moment. We've finally got fed up of people asking
why we're not at version 1 yet, so you'll see that the version bump is a little
larger than normal on this release. SeqMonk has been plenty stable for several
years already so I guess it's justified.
This release brings in some new features and some updates to existing features
which should make it easier to work with.
- Added a new setup screen the first time the program is run to try to make
it easier to set sensible locations for the cache and genomes folders.
- Added the ability to generate PCA plots to compare data stores, and use
the rotations in a given PC to select sets of probes which characterise that
PC.
- Added a probe list collation filter to make it easy to intersect large
numbers of probe lists. Renamed the old combine filter to 'logically combine'
- Improved BedGraph export so you can now output multiple files in one go and
made them immediately compatible with bedGraphToBigWig so you can more easily
load them into UCSC browser.
- Fixed a bug in the quantitation of probes using the new multi-genome projects
- Added a duplication quantitation
- Cleaned up and removed a load of functions in the menus which we're pretty
sure no one ever used.
- Fixed a bug on windows systems when the Documents folder was set to be the
seqmonk genomes folder. Got to learn a lot about the madness of windows
junction files.
- Allow the per-probe normalisation to use either the median or the mean
- Fixed a bug when importing HiC data from BAM files and applying a MAPQ
filter.
RELEASE NOTES FOR SeqMonk v0.34.1
---------------------------------
This release is a bugfix release which addresses 3 problems found in the last
release.
1) Fixed a crash in the beanplot where the quantitated value for the first
probe in a set is null.
2) Fixed a problem where you couldn't select small chromosomes in the genomes
view.
3) Fixed a hang when trying to move to very short probe positions from a report.
RELEASE NOTES FOR SeqMonk v0.34.0
---------------------------------
This release adds a couple of new features which might be useful for the analysis
of some data types and adds some fixes and improvements.
* We've added some tools to help with the analysis of transcription termination.
These include a termination quantitaiton which looks at the proportional loss
of read signal as you pass a putative termination site at the end of a transcript.
We also have a statistical test for this where we use a contingency test to
test whether the loss of read counts is significant or not.
* In the read position probe generator you can now design probes just within
a target region or within an existing probe list.
* We've added a new beanplot display which is much better for looking at the
overall structure of multiple genomes than the boxwhisker plot we had been
using up to this point.
* We've changed the default options for the import of BAM files. SeqMonk will now
set the default MAPQ filter value to 20 rather than having it default to
zero. If no read in the first 100,000 in the file has a MAPQ >=20 then the
filter will be set to the maximum observed MAPQ value. In most cases this
will mean that only high quality alignments will be imported. You should
check that the value detected makes sense with the aligner you used though
as some files may not produce a sensible value from the first 100k reads.
If you want to keep the previous behaviour (no MAPQ filtering) you should
either delete the MAPQ value, or set it to 0.
* We fixed a bug in v0.33.0 where it couldn't reimport data which came from v0.33.0
* We've added a new shortcut (Control+I) to trigger an import from BAM file
* We've changed the behaviour of most plots regarding how they treat the display
of replicate sets. For a while we've had the ability to exand replicate sets
in the chromosome view so you could see the individual replicates rather than
looking at the mean (this is configurable in the display preferences). We've
now made it so that in all plots which pick up their data stores based on what's
visible, and which aren't displaying variance information, we will make them
show the individual stores within the replicate set if the option to expand
replicate sets is turned on the display preferences.
* We fixed a bug in the calculation of the total quantitaiton value in the datastore
summary report. A floating point precision problem meant that this value could
end up being inaccurate when large numbers of small integers were quantitated.
* We've changed the display of remote genomes in the import genomes step to show the
date at which the genomes were created so you can cite this if you want to know
exactly which version of the Ensembl annotations were used for a given genome
assembly.
RELEASE NOTES FOR SeqMonk v0.33.0
---------------------------------
This release is a major release which introduces some significant new functionality
to the program, much of it designed to make it easier to work with very large
datasets, most of which are likely to be single-cell data. Major changes in this
release are:
* The addition of a new chromosome view report which allows for the bulk export
of chromosome views around a set of probes to be exported.
* Improved the ability of the RNA-Seq pipeline to detect isoform to merge when
using non-Ensembl genome annotations.
* Improved the RNA-Seq QC report to add some new metrics, and to allow the
selection and tagging of samples with poor looking QC.
* Changed the data store tree to allow the samples to be re-ordered in the
chromomosome view based on the tree, or to split stores into replicate sets
based on their clustering within the tree.
* Added a new probe list generator - the shuffled probe list generator which
randomly repositions an existing set of probes.
* Added an option to the auto-split tool to let it be case insensitive
* Changed the genome selector to be alphabetically ordered
* Added an option to the data set editor to revert all names to the original file
names.
* Made the aligned probes plot support multiple probe lists and also use consistent
scaling.
* Made the scaling consistent between all sub-plots in a box whisker and star wars
plot collection.
* Added a data export option to the box whisker plot.
* Added probe names to the Hierarchical cluster plot.
* Added a variance plot to look at variability within a replicate set
* Added a variance filter to select probes based on their variability
* Added an intensity difference variance filter to identify probes with unusually high
variability
* Fixed a problem where the chromosome view couldn't be resized if too many tracks were loaded
* Made it so that a data track will have a minimum size if it has been selected from the
data view
* Added an option to have add-in control genomes which can supplement any standard genome.
Started by adding in a genome for ERCC spike-in controls.
* Fixed a bug where gff3 files weren't being loaded in custom genomes
* Made the duplication plot work across multiple data stores at once.
RELEASE NOTES FOR SeqMonk v0.32.1
---------------------------------
This release provides a fix seen on some systems where all R sessions displaying
the R console would hang. In addition this release greatly improves the reporting
of R crashes so that the full R log file is now automatically sent with the
crash report and users don't have to retrieve this separately.
We have also fixed a number of layout issues in the interface where on some
systems some buttons or options might not be visible on screen without making
dialogs or windows larger. This particularly affected projects using very long
dataset or group names. We know that there are more of this type of issue
in the program and will keep working to fix all of these, but if you do hit
this issue, please report which dialog you saw it in so we can make sure we