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- 20:40, 22 November 2024 Projects (hist | edit) [5,237 bytes] Vishal.bakshi (talk | contribs) (Created page with "{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}} __NOTOC__ <!-- BANNER ACROSS TOP OF PAGE --> <div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"> <div style="margin:0.4em; text-align:center;"> <div style="font-size:160%; padding:.1e...")
- 16:32, 22 November 2024 Main Page/test (hist | edit) [519 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}} __NOTOC__ <!-- BANNER ACROSS TOP OF PAGE --> <div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"> <div style="margin:0.4em; text-align:center;"> <div style="font-size:160%; padding:.1e...")
- 14:42, 17 October 2024 Major updates to the BioXpress from the previous version (v-4.0) (hist | edit) [3,857 bytes] Hivelabwikiadmin (talk | contribs) (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...")
- 14:59, 16 October 2024 BioXpress pipeline README (hist | edit) [20,295 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "hi")
- 22:47, 9 October 2024 Additional Notes - tcga (hist | edit) [2,216 bytes] Hivelabwikiadmin (talk | contribs) (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 |...")
- 22:06, 9 October 2024 Additional notes- CIVIC (hist | edit) [5,388 bytes] Hivelabwikiadmin (talk | contribs) (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...")
- 22:02, 9 October 2024 Additional Notes for COSMIC (hist | edit) [2,945 bytes] Hivelabwikiadmin (talk | contribs) (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...")
- 21:56, 9 October 2024 Final Fields (hist | edit) [857 bytes] Hivelabwikiadmin (talk | contribs) (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...")
- 21:33, 9 October 2024 Common fields for VCF files (hist | edit) [554 bytes] Hivelabwikiadmin (talk | contribs) (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...")
- 21:23, 9 October 2024 Additional Notes (hist | edit) [2,115 bytes] Hivelabwikiadmin (talk | contribs) (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...")
- 21:04, 9 October 2024 Additional notes (hist | edit) [5,388 bytes] Hivelabwikiadmin (talk | contribs) (Created page with "Additional notes")
- 13:58, 7 October 2024 GW-FEAST (hist | edit) [863 bytes] Hivelabwikiadmin (talk | contribs) (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...") originally created as "FEAST-ARPA-H"
- 23:38, 30 September 2024 TCGA Additional Information (hist | edit) [1,184 bytes] Hivelabwikiadmin (talk | contribs) (Initial edit)
- 23:10, 30 September 2024 List of TCGA studies (hist | edit) [1,658 bytes] Hivelabwikiadmin (talk | contribs) (Initial edit)
- 19:49, 27 September 2024 BioMuta pipeline README (hist | edit) [20,769 bytes] Hivelabwikiadmin (talk | contribs) (Initial edit)