update readmes for deprecated modules, remove unused modules #481
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only documentation updates. |
zzgeng
reviewed
Dec 11, 2023
analyses/README.md
Outdated
| | [long-format-table-utils](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/master/analyses/long-format-table-utils) (**DEPRECATED**) | `ensg-hugo-rmtl-mapping.tsv` `analyses/fusion_filtering/references/genelistreference.txt` `efo-mondo-map.tsv` `uberon-map-gtex-group.tsv` `uberon-map-gtex-subgroup.tsv` | Functions and scripts for handling long-format tables | No | `annotator/annotation-data/ensg-gene-full-name-refseq-protein.tsv` `annotator/annotation-data/oncokb-cancer-gene-list.tsv` | Yes | GitHub | N/A | | ||
| | [methylation-preprocessing](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/master/analyses/methylation-preprocessing) (**DEPRECATED**) | `TARGET_Normal_MethylationArray_20160812.sdrf.txt` `TARGET_NBL_MethylationArray_20160812.sdrf.1.txt` `TARGET_NBL_MethylationArray_20160812.sdrf.2.txt` `TARGET_CCSK_MethylationArray_20160819.sdrf.txt` `TARGET_OS_MethylationArray_20161103.sdrf.txt` `TARGET_WT_MethylationArray_20160831.sdrf.txt` `TARGET_AML_MethylationArray_20160812_450k.sdrf.1.txt` `TARGET_AML_MethylationArray_20160812_450k.sdrf.2.txt` `TARGET_AML_MethylationArray_20160812_27k.sdrf.1.txt` `TARGET_AML_MethylationArray_20160812_27k.sdrf.2.txt` `TARGET_AML_MethylationArray_20160812_27k.sdrf.3.txt` `manifest_methylation_CBTN_20220410.1.csv` `manifest_methylation_CBTN_20220410.2.csv` `manifest_methylation_CBTN_20220410.3.csv` `manifest_methylation_CBTN_20220410.4.csv` | Preprocess probe hybridization intensity values of selected methylated and unmethylated cytosine (CpG) loci into usable methylation measurements for the Pediatric Open Targets, OpenPedCan-analysis raw DNA methylation array datasets. | No | N/A | Yes | Cavatica | N/A | | ||
| | [methylation-summary](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/master/analyses/methylation-summary) (**DEPRECATED**) | `infinium.gencode.v39.probe.annotations.tsv.gz` `independent-specimens.rnaseqpanel.eachchort.tsv` `independent-specimens.methyl.eachcohort.tsv` `gene-expression-rsem-tpm-collapsed.rds` `rna-isoform-expression-rsem-tpm.rds` `methyl-beta-values.rds` `efo-mondo-map.tsv` `histlogies.tsv` | Summarize preprocessed Illumina Infinium Human Methylation array measurements produced by the OpenPedCan methylation preprocessing module and Illumina infinium methylation array CpG probe coordinates. | No | N/A | No | aws | N/A | | ||
| | [molecular-subtyping-ATRT](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/master/analyses/molecular-subtyping-ATRT) | `histologies.tsv` | Molecular subtyping of ATRT samples | No | NA | GitHub | N/A | | |
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I think here should be histologies-base.tsv
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docs only, GA not required |
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Purpose/implementation Section
What scientific question is your analysis addressing?
This PR updates the readmes for the deprecated MTP modules, removes modules no longer used in either OpenPBTA/OpenPedCan and will not be used in the future, and adds PB subtyping to the analysis readme since it was missed.
What was your approach?
Closes #426
What GitHub issue does your pull request address?
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Is there anything that you want to discuss further?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Results
What types of results are included (e.g., table, figure)?
What is your summary of the results?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.