From f32fe3ac6658d04be2e484f94bb4252794b2c664 Mon Sep 17 00:00:00 2001 From: "Matthew A. Wyczalkowski" Date: Fri, 16 Apr 2021 15:02:01 -0500 Subject: [PATCH] Adding new uploads to documentation --- DCC_Analysis_Summary/README.Y3.md | 50 +++++++++++++++---------------- DCC_Analysis_Summary/README.md | 25 ++++++++-------- 2 files changed, 38 insertions(+), 37 deletions(-) diff --git a/DCC_Analysis_Summary/README.Y3.md b/DCC_Analysis_Summary/README.Y3.md index c698996..4ffffdf 100644 --- a/DCC_Analysis_Summary/README.Y3.md +++ b/DCC_Analysis_Summary/README.Y3.md @@ -1,40 +1,40 @@ -Last updated: 2/18/21 +Last updated: 4/15/21 -**Bold fields** are new since 20210115 +**Bold fields** are new since 20210318 ## Analysis Summaries - Case counts - Y3 only Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total --- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | --- -Methylation Array | 43 | 222 | 8 | 116 | 111 | 113 | 229 | 164 | 19 | 246 | 1271 -RNA-Seq Expression | 42 | 222 | 8 | 118 | 111 | 113 | 229 | 164 | 19 | 249 | 1275 -RNA-Seq Fusion | 0 | 110 | 0 | 0 | 0 | 0 | 0 | 81 | 0 | 167 | 358 -RNA-Seq Transcript + Splicing | 0 | 110 | 0 | 0 | 0 | 0 | 0 | 81 | 0 | 167 | 358 -WGS CNV Somatic | 0 | 105 | 0 | 115 | 111 | 113 | 0 | 166 | 0 | 239 | 849 -WGS SV | 0 | 222 | 0 | 56 | 111 | 85 | 0 | 89 | 0 | 200 | 854 -miRNA-Seq | 4 | **43**| 3 | 14 | 22 | 15 | 72 | 82 | 0 | 32 | **287** -WXS MSI | 0 | 117 | 0 | 0 | 0 | 0 | 0 | 166 | 0 | 101 | 384 -WXS Somatic | 0 | **40** | 0 | 0 | 0 | 113 | 0 | 0 | 0 | 0 | **153** -WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 0 | 166 | 0 | 244 | 523 - +Methylation Array | 43 | 222 | 8 |**169**| 111 | 113 | 229 | 164 | 19 | 249 | **1327** +RNA-Seq Expression | 42 | 222 | 8 |**176**| 111 | 113 | 229 | 164 | 19 | 252 | **1336** +RNA-Seq Fusion | 0 | 110 | 0 | 0 | 0 | 0 | 0 | 81 | 0 | 170 | 361 +RNA-Seq Transcript + Splicing | 0 | 110 | 0 |**69**| 0 | 0 |**109**| 81 | 0 | 170 | 539 +WGS CNV Somatic | 0 | 146 | 0 | 115 | 111 | 113 | 0 | 166 | 0 | 242| 893 +WGS SV | 0 | 222 | 0 |**114**| 111 | 85 |**109**| 89 | 0 | 203 | **1024** +miRNA-Seq | 4 | 43| 3 | 14 | 22 | 15 | 72 | 82 | 0 | 35 | 290 +WXS MSI | 0 | 156 | 0 | 0 | 0 | 0 | 0 | 166 | 0 | 104 | 426 +WXS Somatic TD | 0 | 0 | 0 |**57**| 0 | 113 |**109**| 0 | 0 | 0 | **279** +WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 0 | 166 | 0 | 247 | 526 +WXS Germline | 0 | 110 | 0 |**157**|110 | 110 |**218**| 145 | 0 | 95 | **945** ## All results (Y1, Y2, Y3) - Case counts Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total --- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | --- -Methylation Array | 43 | 222 | 8 | 116 | 111 | 113 | 229 | 164 | 19 | 246 | 1271 -miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 247 | 1269 -RNA-Seq Expression | 42 | 225 | 8 | 120 | 118 | 117 | 230 | 164 | 19 | 251 | 1275 -RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 244 | 1174 -RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 119 | 111 | 113 | 53 | 164 | 0 | 244 | 1029 -WGS SV | 0 | 222 | 0 | 115 | 132 | 113 | 111 | 166 | 0 | 239 | 1168 -WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 239 | 1087 -WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 244 | 1085 -WXS Normal Adjacent | 0 | 80 | 0 | 0 | 5 | 22 | 101 | 0 | 0 | 21 | 229 -WXS Somatic | 0 | **40** | 0 | 0 | 0 | 113 | 0 | 0 | 0 | 0 | **153** -WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 244 | 632 - +Methylation Array | 43 | 222 | 8 | 169 | 111 | 113 | 229 | 164 | 19 | 249 | 1327 +miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 250 | 1272 +RNA-Seq Expression | 42 | 222 | 8 | 176 | 111 | 113 | 229 | 164 | 19 | 252 | 1336 +RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 247 | 1177 +RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 188 | 111 | 113 | 162 | 164 | 0 | 247 | 1167 +WGS SV | 0 | 222 | 0 | 173 | 132 | 113 | 220 | 166 | 0 | 242 | 1337 +WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 242 | 1090 +WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 247 | 1088 +WXS Somatic TD | 0 | 0 | 0 | 57 | 0 | 113 | 109 | 0 | 0 | 0 | 279 +WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 247 | 635 +WXS Germline | 0 | 110 | 0 | 157 |110 | 110 | 218 | 145 | 0 | 95 | 945 + ### Technical Generate Y3 counts with, diff --git a/DCC_Analysis_Summary/README.md b/DCC_Analysis_Summary/README.md index 0a0090f..6cfbe3f 100644 --- a/DCC_Analysis_Summary/README.md +++ b/DCC_Analysis_Summary/README.md @@ -28,19 +28,20 @@ Pipelines which generate multiple result files per case will have multiple entri Counts of cases processed per disease and pipeline. Counts of results to reference other than GDC hg38 excluded. -Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total +Pipeline (last updated 4/15/21) | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total --- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | --- -Methylation Array | 43 | 222 | 8 | 116 | 111 | 113 | 229 | 164 | 19 | 246 | 1271 -miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 247 | 1269 -RNA-Seq Expression | 42 | 225 | 8 | 120 | 118 | 117 | 230 | 164 | 19 | 251 | 1275 -RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 244 | 1174 -RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 119 | 111 | 113 | 53 | 164 | 0 | 244 | 1029 -WGS SV | 0 | 222 | 0 | 115 | 132 | 113 | 111 | 166 | 0 | 239 | 1077 -WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 239 | 1087 -WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 244 | 1085 -WXS Normal Adjacent | 0 | 80 | 0 | 0 | 5 | 22 | 101 | 0 | 0 | 21 | 229 -WXS Somatic | 0 | 0 | 0 | 0 | 0 | 113 | 0 | 0 | 0 | 0 | 113 -WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 244 | 632 +Methylation Array | 43 | 222 | 8 | 169 | 111 | 113 | 229 | 164 | 19 | 249 | 1327 +miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 250 | 1272 +RNA-Seq Expression | 42 | 222 | 8 | 176 | 111 | 113 | 229 | 164 | 19 | 252 | 1336 +RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 247 | 1177 +RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 188 | 111 | 113 | 162 | 164 | 0 | 247 | 1167 +WGS SV | 0 | 222 | 0 | 173 | 132 | 113 | 220 | 166 | 0 | 242 | 1337 +WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 242 | 1090 +WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 247 | 1088 +WXS Somatic TD | 0 | 0 | 0 | 57 | 0 | 113 | 109 | 0 | 0 | 0 | 279 +WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 247 | 635 +WXS Germline | 0 | 110 | 0 | 157 |110 | 110 | 218 | 145 | 0 | 95 | 945 +