User contributions for Hivelabwikiadmin
A user with 152 edits. Account created on 25 September 2024.
17 October 2024
- 14:4614:46, 17 October 2024 diff hist +98 Major updates to the BioXpress from the previous version (v-4.0) →Issue Running DESeq per Case
- 14:4514:45, 17 October 2024 diff hist −69 Major updates to the BioXpress from the previous version (v-4.0) →Issue Running DESeq per Case
- 14:4414:44, 17 October 2024 diff hist +1 Major updates to the BioXpress from the previous version (v-4.0) →Issue Running DESeq per Case
- 14:4214:42, 17 October 2024 diff hist +3,827 N Major updates to the BioXpress from the previous version (v-4.0) Created page with "== Tumor Samples Added for Each Tissue == {| class="wikitable" ! Tissue !! TCGA Studies !! New Samples |- | Bladder || BLCA || 126 |- | Breast || BRCA || 159 |- | Colorectal || COAD/READ || 159 (141/18) |- | Esophageal || ESCA || 25 |- | Head and Neck || HNSC || 118 |- | Kidney || KICH/KIRP/KIRC || 289 (15/82/192) |- | Liver || LIHC || 169 |- | Lung || LUAD/LUSC || 264 (174/90) |- | Prostate || PRAD || 116 |- | Stomach || STAD || 22 |- | Thyroid || THCA || 176 |- | Uteri..."
- 14:3914:39, 17 October 2024 diff hist +103 BioXpress pipeline README →Publisher Step 2: Run the script de-publish-per-tissue.py
- 14:3714:37, 17 October 2024 diff hist +2,496 BioXpress pipeline README →DESeq Step 3: Run the script run_per_case.sh
- 14:3414:34, 17 October 2024 diff hist +4,847 BioXpress pipeline README →Output
- 14:2314:23, 17 October 2024 diff hist +2 BioXpress pipeline README →Output
- 14:2314:23, 17 October 2024 diff hist +2 BioXpress pipeline README →Method
- 14:2314:23, 17 October 2024 diff hist +2 BioXpress pipeline README →Summary
- 14:2214:22, 17 October 2024 diff hist +2 BioXpress pipeline README →Annotation Step 3: Run the script split_per_case.py
- 14:2114:21, 17 October 2024 diff hist +2,014 BioXpress pipeline README →Output
- 14:2114:21, 17 October 2024 diff hist +177 BioXpress pipeline README →Method
- 14:1814:18, 17 October 2024 diff hist −17 BioXpress pipeline README →Method
- 14:1814:18, 17 October 2024 diff hist −68 BioXpress pipeline README →Method
- 14:1714:17, 17 October 2024 diff hist −18 BioXpress pipeline README →Method
- 14:1514:15, 17 October 2024 diff hist +1,970 BioXpress pipeline README →Method
- 14:1314:13, 17 October 2024 diff hist +1,241 BioXpress pipeline README →Output
16 October 2024
- 17:4817:48, 16 October 2024 diff hist +3 BioXpress pipeline README →Method
- 17:4717:47, 16 October 2024 diff hist +110 BioXpress pipeline README →Summary
- 17:4717:47, 16 October 2024 diff hist +1 BioXpress pipeline README →Output
- 17:4617:46, 16 October 2024 diff hist −2,415 BioXpress pipeline README →BioXpress Downloader Step
- 17:4617:46, 16 October 2024 diff hist −102 BioXpress pipeline README →Method
- 17:4417:44, 16 October 2024 diff hist +9 BioXpress pipeline README →Method
- 17:4217:42, 16 October 2024 diff hist +3 BioXpress pipeline README →Method
- 17:3817:38, 16 October 2024 diff hist +1 BioXpress pipeline README →General Flow of Scripts
- 17:2317:23, 16 October 2024 diff hist +887 BioXpress pipeline README →Method
- 17:1917:19, 16 October 2024 diff hist +852 BioXpress pipeline README →Method
- 17:1817:18, 16 October 2024 diff hist +2 BioXpress pipeline README →Method
- 17:1817:18, 16 October 2024 diff hist +351 BioXpress pipeline README →BioXpress Downloader Step
- 17:0517:05, 16 October 2024 diff hist +1,615 BioXpress pipeline README →General Flow of Scripts
- 17:0417:04, 16 October 2024 diff hist +552 BioXpress pipeline README →Method
- 17:0417:04, 16 October 2024 diff hist +825 BioXpress pipeline README No edit summary
- 15:2015:20, 16 October 2024 diff hist +924 BioXpress pipeline README No edit summary
- 15:0415:04, 16 October 2024 diff hist +907 BioXpress pipeline README No edit summary
- 15:0115:01, 16 October 2024 diff hist +394 BioXpress pipeline README No edit summary
- 14:5914:59, 16 October 2024 diff hist +2 N BioXpress pipeline README Created page with "hi"
9 October 2024
- 22:4722:47, 9 October 2024 diff hist −2,218 BioMuta pipeline README →Additional Notes
- 22:4722:47, 9 October 2024 diff hist +2,216 N Additional Notes - tcga Created page with "=== Additional Notes === All the mapping files are available in the repository folder: `pipeline/convert_step2/mapping` The mapping files used for converting TCGA are: '''DOID:''' * `tcga_doid_mapping.csv` TCGA Projects were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping): {| class="wikitable" ! DO_slim_id ! DO_slim_name ! TCGA_project |- | DOID:5041 | esophageal cancer | TCGA-ESCA |- | DOID:2531 | hematologic cancer |..." current
- 22:4622:46, 9 October 2024 diff hist +29 BioMuta pipeline README →Usage
- 22:3722:37, 9 October 2024 diff hist −6 BioMuta pipeline README →Usage
- 22:0622:06, 9 October 2024 diff hist +5,388 N Additional notes- CIVIC Created page with "=== Additional Notes === All the mapping files are available in the scripts repository in the folder: `pipeline/convert_step2/mapping` The mapping files used for converting CIVIC are: '''DOID:''' * `tcga_doid_mapping.csv` CIVIC DOID child terms were mapped to DOID parent terms using the following table (generated from the OncoMX DOID mapping table): {| class="wikitable" ! CIVIC Entity Disease |- | Acral_Lentiginous_Melanoma_(DOID_6367) |- | Acute_Lymphoblastic_Leukem..." current
- 22:0522:05, 9 October 2024 diff hist +12 BioMuta pipeline README →Run map_civic_csv.py
- 22:0322:03, 9 October 2024 diff hist +2 BioMuta pipeline README →Example Line Transformation
- 22:0222:02, 9 October 2024 diff hist +2,945 N Additional Notes for COSMIC Created page with "=== Additional Notes === All the mapping files are available in the scripts repository in the folder: `pipeline/convert_step2/mapping` The mapping files used for converting the COSMIC tsv are: '''DOID:''' * `cosmic_doid_mapping.csv` COSMIC tissue site terms were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping): {| class="wikitable" ! Primary Site ! Top_Level_Organ_system |- | NS | NA |- | adrenal_gland | DOID:3953 / adre..." current
- 22:0122:01, 9 October 2024 diff hist +10 BioMuta pipeline README →Usage
- 21:5921:59, 9 October 2024 diff hist +114 BioMuta pipeline README →Script Specifications
- 21:5621:56, 9 October 2024 diff hist +857 N Final Fields Created page with "=== Additional Notes === ==== Final fields ==== {| class="wikitable" ! Field ! Description |- | sample_name | Sample ID provided by the original resource (for v-5.0 only applies to TCGA and COSMIC) |- | chr_id | Chromosome number only (no ‘chr’) |- | start_pos | Genomic coordinates (For v-5.0 these are all with ref GRCh38) |- | end_pos | Identical to the start position because all mutations are Specifications |- | ref_nt | Reference nucleotide |- | alt_nt | Nucleot..." current
- 21:5521:55, 9 October 2024 diff hist −4 BioMuta pipeline README →Usage
- 21:5421:54, 9 October 2024 diff hist +22 BioMuta pipeline README →Usage