User contributions for Hivelabwikiadmin
A user with 116 edits. Account created on 25 September 2024.
16 October 2024
- 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 current
- 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
- 21:5321:53, 9 October 2024 diff hist +935 BioMuta pipeline README →Step 3: Combine
- 21:5021:50, 9 October 2024 diff hist −830 Additional Notes →Additional Notes current
- 21:4721:47, 9 October 2024 diff hist +1,085 BioMuta pipeline README →Usage
- 21:4321:43, 9 October 2024 diff hist +22 BioMuta pipeline README →Usage
- 21:4221:42, 9 October 2024 diff hist −15 BioMuta pipeline README →Other files used
- 21:3921:39, 9 October 2024 diff hist −8 BioMuta pipeline README →Requirements
- 21:3721:37, 9 October 2024 diff hist −50 BioMuta pipeline README →Genomic Liftover Notes
- 21:3321:33, 9 October 2024 diff hist +554 N Common fields for VCF files Created page with " {| class="wikitable" ! Field ! Description |- | Chrom | chromosome that the variation is being called on |- | Pos | base position of the variant |- | ID | identifier of the variant |- | Ref | reference base at the position of variance |- | Alt | alternate alleles at the position |- | Qual | quality score of the given alleles |- | Filter | indicates which set of filters failed or passed |- | Info | descriptions of the variation |- | Format | (optional) fields describing..." current
- 21:3221:32, 9 October 2024 diff hist +5,004 BioMuta pipeline README →Usage
- 21:2321:23, 9 October 2024 diff hist +2,945 N Additional Notes 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..."
- 21:2121:21, 9 October 2024 diff hist +22 BioMuta pipeline README →Usage
- 21:1921:19, 9 October 2024 diff hist +1,262 BioMuta pipeline README →Usage
- 21:0921:09, 9 October 2024 diff hist +5,372 Additional notes No edit summary current
- 21:0421:04, 9 October 2024 diff hist +16 N Additional notes Created page with "Additional notes"
- 21:0321:03, 9 October 2024 diff hist +22 BioMuta pipeline README →Usage
- 20:2520:25, 9 October 2024 diff hist −7 BioMuta pipeline README →Usage
- 20:2420:24, 9 October 2024 diff hist +4 BioMuta pipeline README →Example Line Transformation
- 20:2420:24, 9 October 2024 diff hist +3 BioMuta pipeline README →Example Line Transformation
- 20:2320:23, 9 October 2024 diff hist +3,565 BioMuta pipeline README →Convert: TCGA
- 15:3515:35, 9 October 2024 diff hist −326 BioMuta pipeline README →Additional Notes
- 15:2215:22, 9 October 2024 diff hist +2,796 BioMuta pipeline README →Usage
- 15:1115:11, 9 October 2024 diff hist +1,234 BioMuta pipeline README →Step 2: Convert
- 15:0415:04, 9 October 2024 diff hist +174 BioMuta pipeline README →Pipeline Overview
- 15:0215:02, 9 October 2024 diff hist +1,280 BioMuta pipeline README →Download: COSMIC
7 October 2024
- 13:5813:58, 7 October 2024 diff hist +881 N GW-FEAST Created page with "GW-FEAST Project The GW Federated Ecosystems for Analytics and Standardized Technologies (GW-FEAST) project is part of the ARPA-H FEAST performer team initiative that includes academic and industry partners. The goal of the ARPA-H performer teams is “to create bridges across data silos to make health data more accessible and usable”. ARPA-H FEAST offers two major innovations for digital healthcare ecosystems addressing current challenges. 1) Agnostic federation ac..."
2 October 2024
- 16:2316:23, 2 October 2024 diff hist +99 m BioMuta pipeline README Added sharepoint link
1 October 2024
- 14:1114:11, 1 October 2024 diff hist +1,675 BioMuta pipeline README Download: TCGA
30 September 2024
- 23:3823:38, 30 September 2024 diff hist +1,184 N TCGA Additional Information Initial edit current
- 23:1023:10, 30 September 2024 diff hist +1,658 N List of TCGA studies Initial edit current
- 21:3321:33, 30 September 2024 diff hist +1,636 BioMuta pipeline README Download: TCGA
- 21:2521:25, 30 September 2024 diff hist −1 m Template:Inline-code debugging current
- 21:2521:25, 30 September 2024 diff hist −9 m Template:Inline-code fixed code
- 21:2421:24, 30 September 2024 diff hist +50 Template:Inline-code Included documentation
- 21:2121:21, 30 September 2024 diff hist −40 m Template:Documentation debugging current
- 21:1721:17, 30 September 2024 diff hist −25 m Template:Documentation troubleshooting
- 21:0921:09, 30 September 2024 diff hist +2 m Template:Documentation Trying to get it to work