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#645 Part 1: Documentation only #659
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This was referenced Mar 28, 2020
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jaclyn-taroni
changed the title
kgaonkar6
reviewed
Mar 30, 2020
analyses/README.md
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| @@ -20,19 +20,21 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist | |||
| | [`create-subset-files`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/create-subset-files) | All files | This module contains the code to create the subset files used in continuous integration | All subset files for continuous integration | |||
| | [`focal-cn-file-preparation`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/focal-cn-file-preparation) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz` | Maps from copy number variant caller segments to gene identifiers; will be updated to take into account changes that affect entire cytobands, chromosome arms ([#186](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/186))| `results/cnvkit_annotated_cn_autosomes.tsv.gz` <br> `results/cnvkit_annotated_cn_x_and_y.tsv.gz` <br> `results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `results/controlfreec_annotated_cn_x_and_y.tsv.gz` <br> `results/consensus_seg_annotated_cn_autosomes.tsv.gz` (included in data download) <br> `results/consensus_seg_annotated_cn_x_and_y.tsv.gz` (included in data download) | |||
| | [`fusion_filtering`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion_filtering) | `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Standardizes, filters, and prioritizes fusion calls | `results/pbta-fusion-putative-oncogenic.tsv`(included in data download) <br> `results/pbta-fusion-recurrent-fusion-byhistology.tsv` (included in data download) <br> `results/pbta-fusion-recurrent-fusion-bysample.tsv` (included in data download) | |||
| | [`fusion-summary`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion-summary)| `pbta-histologies.tsv` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Generate summary tables from fusion files ([#398](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398)) | `results/fusion_summary_embryonal_foi.tsv` (included in data download) <br> `results/fusion_summary_ependymoma_foi.tsv` (included in data download) | |||
| | [`fusion-summary`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion-summary)| `pbta-histologies.tsv` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Generate summary tables from fusion files ([#398](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398)) | `results/fusion_summary_embryonal_foi.tsv` (included in data download) <br> `results/fusion_summary_ependymoma_foi.tsv` (included in data download) <br> `results/fusion_summary_ewings_foi.tsv` | |||
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| | [`fusion-summary`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion-summary)| `pbta-histologies.tsv` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Generate summary tables from fusion files ([#398](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398)) | `results/fusion_summary_embryonal_foi.tsv` (included in data download) <br> `results/fusion_summary_ependymoma_foi.tsv` (included in data download) <br> `results/fusion_summary_ewings_foi.tsv` | |
| | [`fusion-summary`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion-summary)| `pbta-histologies.tsv` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Generate summary tables from fusion files ([#398](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398)) <br> Proposed Analysis: Identify CNS Ewing Sarcomas ([#623](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/623)) | `results/fusion_summary_embryonal_foi.tsv` (included in data download) <br> `results/fusion_summary_ependymoma_foi.tsv` (included in data download) <br> `results/fusion_summary_ewings_foi.tsv` |
should we add the ewings sarcoma fusion summary issue here as well?
Co-Authored-By: Krutika Gaonkar <34580719+kgaonkar6@users.noreply.github.com>
5 tasks
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@kgaonkar6 are there any additional changes you'd like to see? |
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Thanks! Documentation only change, merging w/o CI check! |
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Purpose/implementation Section
Here I'm adding the
What GitHub issue does your pull request address?
#645
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Note that in some cases the changes to the files used or output by the molecular subtyping modules in the modules at a glance table will come in a later pull request. This is up-to-date with everything that I currently expect to land as part of breaking up #658.
Which areas should receive a particularly close look?
analyses/molecular-subtyping-pathology/README.mdReproducibility Checklist
Documentation only changes!
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.