Merge pull request #27 from logstar/rna-seq-cg-stat

Calculate TPM mean/z-score/SD/quantile summary statistics within each cancer group and cohort

analyses/README.md

@@ -47,6 +47,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | [`rna-seq-composition`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/rna-seq-composition) | `pbta-gene-expression-rsem-tpm.stranded.rds` <br> `pbta-histologies.tsv` <br> `pbta-mend-qc-results.tar.gz` <br> `pbta-mend-qc-manifest.tsv` <br> `pbta-star-log-manifest.tsv` <br> `pbta-star-log-final.tar.gz` | Analyzes the fraction of read types that comprise each RNA-Seq sample; flags samples with unusual composition| N/A
 | [`rna-seq-protocol-ruvseq`](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/rna-seq-protocol-ruvseq) | `gene-counts-rsem-expected_count-collapsed.rds` | Evaluate the use of empirical negative control genes for batch correction | N/A
 | [`rna-seq-protocol-dge`](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/rna-seq-protocol-dge) | `pbta-gene-counts-rsem-expected_count.polya.rds` <br> `pbta-gene-counts-rsem-expected_count.stranded.rds` | *In progress* [PediatricOpenTargets/ticket-tracker#17](https://github.com/PediatricOpenTargets/ticket-tracker/issues/17); check if the DGE analysis between poly-A and stranded RNA-seq data follow a null-p-value distribution; determine stably expressed genes between poly-A and stranded samples.| N/A
+| [`rna-seq-expression-summary-stats`](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/rna-seq-expression-summary-stats) | `gene-expression-rsem-tpm-collapsed.rds` <br> `histologies.tsv` | Calculate TPM summary statistics within each cancer group and cohort. [PediatricOpenTargets/ticket-tracker#51](https://github.com/PediatricOpenTargets/ticket-tracker/issues/51). | N/A
 | [`run-gistic`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/run-gistic) | `pbta-histologies.tsv` <br> `pbta-cnv-consensus.seg.gz` | Runs GISTIC 2.0 on SEG files | `pbta-cnv-consensus-gistic.zip` (included in data download)
 | [`sample-distribution-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sample-distribution-analysis) | `pbta-histologies.tsv` | Produces plots and tables that illustrate the distribution of different histologies in the PBTA data | N/A
 | [`selection-strategy-comparison`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/selection-strategy-comparison) | `pbta-gene-expression-rsem-fpkm.polya.rds` <br> `pbta-gene-expression-rsem-fpkm.stranded.rds` | *Deprecated*; Comparison of RNA-seq data from different selection strategies | N/A