cognoma cancer-data issues

cognoma / cancer-data

TCGA data acquisition and processing for Project Cognoma

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issues

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Add cancer-type codes to mapping

#48 gwaybio closed 6 years ago
3
Add recurrent solid & metastatic samples

#47 dhimmel closed 6 years ago
2
Retain Metastatic Tumors

#46 gwaybio closed 6 years ago
6
Move diseases.tsv to data

#45 dhimmel closed 6 years ago
1
Retain zero-mutation samples

#44 dhimmel closed 6 years ago
7
Filtering samples is (potentially) too strict

#43 gwaybio closed 6 years ago
22
Modernize repo: readme updates & LFS

#42 dhimmel closed 6 years ago
3
Update Data for April 2018 TCGA PanCanAtlas Data Release

#41 gwaybio closed 6 years ago
2
TCGA PanCanAtlas Paper/Data Release

#40 gwaybio closed 6 years ago
12
Treehouse Childhood Cancer Initiative

#39 gwaybio opened 6 years ago
5
Much Richer Sample Clinical Data

#38 gwaybio opened 7 years ago
9
Recurrence and Distant Metastasis

#37 binaypanda opened 7 years ago
1
Invalid gene in mutation-matrix.tsv.bz2 on figshare v5

#36 dhimmel closed 7 years ago
1
Melt mutation matrix for use by core-service repository.

#35 stephenshank closed 7 years ago
1
Reshape mutation matrix for use by core-service repository

#34 stephenshank closed 4 years ago
3
Dual license repository as BSD & CC0

#33 dhimmel closed 7 years ago
1
Outsource Entrez Gene logic to cognoma/genes

#32 dhimmel closed 7 years ago
6
Compute differential expression (tumor versus normal in paired samples) for cancers

#31 dhimmel opened 7 years ago
7
Extract gene information

#30 dhimmel closed 7 years ago
2
[WIP] Create JSON files for frontend consumption

#29 dhimmel opened 7 years ago
4
Export complete data

#28 dhimmel closed 7 years ago
0
Add disease acronyms and update covariates.tsv

#27 dhimmel closed 7 years ago
2
Acronyms for diseases

#26 dhimmel closed 7 years ago
8
Create sample-by-pathway dataset

#25 stephenshank closed 4 years ago
2
Encodes categorical covariates from samples dataset.

#24 stephenshank closed 7 years ago
0
Export a gene information table

#23 dhimmel closed 7 years ago
1
Add exploratory analyses of mutation data

#22 dhimmel closed 7 years ago
9
Precomputing a sample × mutation-in-gene-set matrix

#21 stephenshank opened 7 years ago
7
Extract sample info from PANCAN_clinicalMatrix

#20 dhimmel closed 7 years ago
13
Add figshare link to README

#19 dhimmel closed 7 years ago
1
Sanitize notebook cell numbers, update HiSeqV2

#18 dhimmel closed 7 years ago
2
Generate comprehensive comparisons between RNAseq, Mutation, and Clinical Matrix

#17 gwaybio closed 7 years ago
2
Current Xena PANCAN_mutation dataset is missing some samples and variables from a previous release

#16 gwaybio opened 7 years ago
12
Extract detailed mutation information for TCGA samples

#15 gwaybio opened 7 years ago
2
Variable documentation for Xena Browser's PANCAN_clinicalMatrix

#14 Inquisitive-Geek closed 7 years ago
8
Identify the types of clinical data fields for the django team

#13 cgreene opened 7 years ago
2
Map mutation gene symbols to Entrez IDs

#12 clairemcleod closed 7 years ago
12
exploring the data

#11 ypar opened 7 years ago
3
Process the clinical matrix to extract sample attributes

#10 ypar closed 7 years ago
10
Persistent storage of matrices that enables quick indexed lookup

#9 dhimmel opened 7 years ago
4
Map HiSeqV2 symbols to entrez gene IDs

#8 dhimmel closed 7 years ago
4
Process data into expression and mutation matrices

#7 dhimmel closed 7 years ago
5
Converting Xena datasets to standard identifiers rather than gene symbols

#6 dhimmel closed 7 years ago
7
Repository licensing options that are appropriate for non-code content

#5 dhimmel closed 7 years ago
9
Gene names converted to dates in Xena's PANCAN_mutation dataset

#4 dhimmel opened 7 years ago
5
Licensing of the Xena TCGA Pan-Cancer Data

#3 dhimmel closed 7 years ago
6
Which types of mutation effects should be ignored?

#2 dhimmel opened 7 years ago
5
Create a data/notebook repository framework and download TCGA data

#1 dhimmel closed 7 years ago
1