Updated analysis: RNA summary files and base histology subtyping update for v18

[kgaonkar6]

What analysis module should be updated and why?

RNA-seq summary files generation modules part of download or used in subtyping

Module	Reason	Brief Description	output
collapse-rnaseq	adding 8 samples #749 and used in subtyping	Collapses RSEM FPKM matrices such that gene symbols are de-duplicated.	results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds (included in data download; too large for tracking via GitHub) results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds (included in data download; too large for tracking via GitHub)
fusion_filtering	adding 8 samples #749 and used in subtyping	Standardizes, filters, and prioritizes fusion calls updated in #808 and #830	results/pbta-fusion-putative-oncogenic.tsv(included in data download) results/pbta-fusion-recurrent-fusion-byhistology.tsv (included in data download) results/pbta-fusion-recurrent-fusion-bysample.tsv (included in data download) results/fusion_summary_lgat_foi.tsv (included in data download)
fusion-summary	adding 8 samples #749 and used in subtyping	Generate summary tables from fusion files updated in #812 and #816 and #821 and comment	results/fusion_summary_embryonal_foi.tsv (included in data download) results/fusion_summary_ependymoma_foi.tsv (included in data download) results/fusion_summary_ewings_foi.tsv
gene-set-enrichment-analysis	adding 8 samples #749 and used in subtyping	Updated gene set enrichment analysis with appropriate RNA-seq expression data	results/gsva_scores_stranded.tsv results/gsva_scores_polya.tsv for stranded, polya expression data respectively
independent-samples	adding 8 samples #749 and used in subtyping	Generates independent specimen lists for WGS/WXS samples updated in #795 and #797 and comment	results/independent-specimens.wgs.primary.tsv (included in data download) results/independent-specimens.wgs.primary-plus.tsv (included in data download) results/independent-specimens.wgswxs.primary.tsv (included in data download) results/independent-specimens.wgswxs.primary-plus.tsv (included in data download) results/independent-specimens.rnaseq.primary-plus-stranded.tsv(included in data download) results/independent-specimens.rnaseq.primary-plus-polya.tsv (included in data download)
transcriptomic-dimension-reduction	adding 8 samples #749 used in subtyping	Dimension reduction and visualization of RNA-seq data	N/A

Subtyping modules

Module	Reason	Brief Description	output
molecular-subtyping-CRANIO	to add subtyping to base histology	Molecular subtyping of craniopharyngiomas samples	results/CRANIO_molecular_subtype.tsv
molecular-subtyping-EPN	to add subtyping to base histology	Molecular subtyping of ependymoma tumors	results/EPN_all_data_withsubgroup.tsv
molecular-subtyping-EWS	to add subtyping to base histology	Reclassification of tumors based on the presence of defining fusions for Ewing Sarcoma per	results/EWS_samples.tsv
molecular-subtyping-HGG	to add subtyping to base histology	Molecular subtyping of high-grade glioma samples	results/HGG_molecular_subtype.tsv
molecular-subtyping-LGAT	to add subtyping to base histology	Molecular subtyping of Low-grade astrocytic tumor samples	results/lgat_subtyping.tsv
molecular-subtyping-MB	to add subtyping to base histology	Molecular classification of Medulloblastoma subtypes	results/MB_molecular_subtype.tsv results/MB_batchcorrected_molecular_subtype.tsv for uncorrected and batch-corrected input matrix
molecular-subtyping-embryonal	to add subtyping to base histology	Molecular subtyping of non-medulloblastoma, non-ATRT embryonal tumors	results/embryonal_tumor_molecular_subtypes.tsv
molecular-subtyping-neurocytoma	to add subtyping to base histology	Molecular subtyping of Neurocytoma samples	results/neurocytoma_subtyping.tsv
molecular-subtyping-pathology	to add subtyping to base histology	Compile output from other molecular subtyping modules and incorporate pathology feedback	results/compiled_molecular_subtyping_with_pathology_feedback.tsv
molecular-subtyping-integrate	to add subtyping to base histology	Add molecular subtype information to base histology	results/pbta-histologies.tsv

What changes need to be made? Please provide enough detail for another participant to make the update.

8 new samples were added, as of v18 we only obtain a QC-ed base histology which we will add combined subtyping from molecular-subtyping-pathology

What input data should be used? Which data were used in the version being updated?

Any stranded RNA-Seq data
All inputs needed for subtyping

When do you expect the revised analysis will be completed?

~ 1 week

Who will complete the updated analysis?

@kgaonkar6

[jaclyn-taroni]

v18 is out, closing this!