smrgit’s gists

smrgit / find_normal_bams_in_gcs.sql

Created September 27, 2017 22:36

join several different metadata tables together to find normal BAMs in GCS, combined with their CGHub and/or GDC file identifiers (where available)

	WITH
	--
	-- first, we grab information about the ~48650 TCGA DNA bam files that were at CGHub
	-- (and are aligned to GRCh37/HG19 and were classified as "Live")
	dbGaPinfo AS (
	SELECT
	SUBSTR(barcode,1,12) AS case_barcode,
	SUBSTR(barcode,1,16) AS sample_barcode,
	barcode AS aliquot_barcode,
	SUBSTR(barcode,14,2) AS sample_type,

smrgit / join_CGHub_GDC_legacy_DNA_bams_info.sql

Created September 28, 2017 11:44

join CGHub and GDC legacy information for TCGA DNA bams

	WITH
	--
	-- first, we grab information about the ~48650 TCGA DNA bam files that were at CGHub
	-- (and are aligned to GRCh37/HG19 and were classified as "Live")
	CGHubInfo AS (
	SELECT
	SUBSTR(barcode,1,12) AS case_barcode,
	SUBSTR(barcode,1,16) AS sample_barcode,
	barcode AS aliquot_barcode,
	SUBSTR(barcode,14,2) AS sample_type,

smrgit / corr_TCGA_GTEx.sql

Created November 28, 2017 23:20

Spearman correlation between TCGA expression data and GTEx median tissue-type TPM

	WITH
	--
	-- get the top-5000 most variable genes based on computing the standard
	-- deviation on the GTEx "gene_median_tpm" table
	GTEx_top5K AS (
	SELECT
	gene_id,
	gene_description,
	STDDEV(gene_exp) AS sigmaExp
	FROM

smrgit / gist:cbba2e057211f3a05d74b0eac0b9fd5f

Created May 24, 2018 15:58

PanCancer Atlas publications -- open-access supplementary files at GDC

smrgit / gist:c170b5659d095a8e01455a358c0b70ee

Created May 24, 2018 16:00

PanCancer Atlas publications -- controlled-access supplementary files at GDC

smrgit / miRNA QC (nb01).ipynb

Created November 9, 2018 20:41

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

Sheila smrgit