Closed logstar closed 1 year ago
Add TCGA RNA-seq samples in OpenPedCan-analysis data release to TPM boxplots. TCGA RNA-seq sample TPM values are in tcga-gene-expression-rsem-tpm-collapsed.rds, and the sample metadata are in histologies.tsv.
tcga-gene-expression-rsem-tpm-collapsed.rds
histologies.tsv
The following design issues have been resolved, but they are still open to suggestions, according to discussions with @jharenza and @chinwallaa in https://opentargetspediatrics.slack.com/archives/C03AR8ZD0RF:
cancer_group
tumor_descriptor
cc @taylordm
Add TCGA RNA-seq samples in OpenPedCan-analysis data release to TPM boxplots. TCGA RNA-seq sample TPM values are in
tcga-gene-expression-rsem-tpm-collapsed.rds
, and the sample metadata are inhistologies.tsv
.The following design issues have been resolved, but they are still open to suggestions, according to discussions with @jharenza and @chinwallaa in https://opentargetspediatrics.slack.com/archives/C03AR8ZD0RF:
cancer_group
inhistologies.tsv
. TCGA boxes do not need to be limited to thecancer_group
s of the pediatric tumor boxes shown in the boxplot, because TCGAcancer_group
s do not match 1:1 to pediatric tumorcancer_group
s, according to @jharenza's comment at https://opentargetspediatrics.slack.com/archives/C03AR8ZD0RF/p1653496395764939?thread_ts=1653494629.301359&cid=C03AR8ZD0RF.cancer_group
s only have primary tumor samples, as suggested by @jharenza at https://opentargetspediatrics.slack.com/archives/C03AR8ZD0RF/p1653497428257809?thread_ts=1653494629.301359&cid=C03AR8ZD0RF. Thetumor_descriptor
s of TCGA samples are checked at https://opentargetspediatrics.slack.com/archives/C03AR8ZD0RF/p1653510453690229?thread_ts=1653494629.301359&cid=C03AR8ZD0RF.cc @taylordm