[AlexsLemonade#229] analyses/README update comparative-rna-seq

analyses/README.md

@@ -15,7 +15,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | [`cnv-chrom-plot`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-chrom) | `pbta-cnv-consensus-gistic.zip` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg` | Makes plots from GISTIC output as well as `seg.mean` plots by histology group  | N/A
 | [`cnv-comparison`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/cnv-comparison) | Earlier version of SEG files | *Deprecated*; compared earlier version of the CNV methods. | N/A
 | [`collapse-rnaseq`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/collapse-rnaseq) | `pbta-gene-expression-rsem-fpkm.polya.rds` <br> `pbta-gene-expression-rsem-fpkm.stranded.rds` <br> `gencode.v27.primary_assembly.annotation.gtf.gz` | Collapses RSEM FPKM matrices such that gene symbols are de-duplicated. | `results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` <br> `results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` (included in data download; too large for tracking via GitHub)
-| [`comparative-RNASeq-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/comparative-RNASeq-analysis) | `pbta-gene-expression-rsem-tpm.polya.rds` <br> `pbta-gene-expression-rsem-tpm.stranded.rds` | *In progress*; will produce expression outlier profiles per [#229](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/229) | N/A |
+| [`comparative-RNASeq-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/comparative-RNASeq-analysis) | `pbta-gene-expression-rsem-tpm.polya.rds` <br> `pbta-gene-expression-rsem-tpm.stranded.rds` <br> `pbta-histologies.tsv` <br> `pbta-mend-qc-manifest.tsv` <br> `pbta-mend-qc-results.tar.gz` | *In progress*; will produce expression outlier profiles per [#229](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/229) | N/A |
 | [`copy_number_consensus_call`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/copy_number_consensus_call) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-sv-manta.tsv.gz` | Produces consensus copy number calls per [#128](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/128) and a set of excluded regions where CNV calls are not made | `results/cnv_consensus.tsv` <br> `results/pbta-cnv-consensus.seg.gz` <br> `ref/cnv_excluded_regions.bed` <br> `ref/cnv_callable.bed`
 | [`create-subset-files`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/create-subset-files) | All files | This module contains the code to create the subset files used in continuous integration | All subset files for continuous integration
 | [`focal-cn-file-preparation`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/focal-cn-file-preparation) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz` | Maps from copy number variant caller segments to gene identifiers; will be updated to take into account changes that affect entire cytobands, chromosome arms ([#186](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/186))| `results/cnvkit_annotated_cn_autosomes.tsv.gz` <br> `results/cnvkit_annotated_cn_x_and_y.tsv.gz` <br> `results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `results/controlfreec_annotated_cn_x_and_y.tsv.gz` <br> `results/consensus_seg_annotated_cn_autosomes.tsv.gz` <br> `results/consensus_seg_annotated_cn_x_and_y.tsv.gz`