Ecosyste.ms: Issues

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GitHub / tcp-lab/transportome_profiler issues and pull requests

#41 - Wrong query in `basic.json`

Issue - State: closed - Opened by Feat-FeAR 3 months ago - 1 comment
Labels: bug

#40 - In `make_genesets.py`, the parameter `min_pop_score` works the other way around

Issue - State: closed - Opened by Feat-FeAR 3 months ago - 1 comment
Labels: bug

#39 - Extract ENSG-HGNC ID correspondences from the MTP-DB

Issue - State: closed - Opened by Feat-FeAR 3 months ago - 2 comments

#38 - Update cancer types for DEA

Pull Request - State: closed - Opened by MrHedmad 3 months ago - 4 comments

#37 - Add shared dysregulation plot

Pull Request - State: closed - Opened by MrHedmad 8 months ago

#36 - Comment why this specific metric was used

Issue - State: closed - Opened by MrHedmad 10 months ago - 1 comment
Labels: documentation

#35 - Add GEO datasets

Pull Request - State: closed - Opened by MrHedmad 12 months ago
Labels: enhancement

#34 - Have reliable pruning

Pull Request - State: closed - Opened by MrHedmad 12 months ago - 1 comment

#33 - Non-deterministic (nor reproducible) pruning.

Issue - State: closed - Opened by Feat-FeAR 12 months ago - 4 comments
Labels: bug, enhancement, wontfix

#32 - Mention the dependency on `jq` in the README

Issue - State: closed - Opened by Feat-FeAR 12 months ago - 1 comment
Labels: documentation

#31 - Missing reference to `fast-cohen` dependency

Issue - State: closed - Opened by Feat-FeAR about 1 year ago
Labels: documentation

#30 - Cleanup selection of tumor types

Pull Request - State: closed - Opened by MrHedmad about 1 year ago

#29 - Review of the queries for the TCGA-GTEX pairing.

Issue - State: closed - Opened by Feat-FeAR about 1 year ago - 1 comment
Labels: enhancement

#28 - Redundancy in `dea_queries.json`

Issue - State: closed - Opened by Feat-FeAR about 1 year ago - 1 comment
Labels: good first issue

#28 - Redundancy in `dea_queries.json`

Issue - State: closed - Opened by Feat-FeAR about 1 year ago - 1 comment
Labels: good first issue

#27 - Cannot run the `heatmaps` pipeline on "test espression matrix"

Issue - State: closed - Opened by Feat-FeAR about 1 year ago - 1 comment
Labels: bug

#26 - Bad hardcoded output path in `metasample.py`

Issue - State: closed - Opened by Feat-FeAR about 1 year ago - 2 comments
Labels: bug

#25 - Rewrite plotting functions

Pull Request - State: closed - Opened by MrHedmad about 1 year ago

#24 - Migrate to Kerblam!

Pull Request - State: closed - Opened by MrHedmad about 1 year ago

#23 - The Log Fold Change calculation is wrong

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: bug

#22 - The DESeq2 Fold Change computation is too slow

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: enhancement, help wanted

#21 - Code review

Issue - State: closed - Opened by MrHedmad over 1 year ago - 2 comments
Labels: enhancement, help wanted

#20 - Add pipeline documentation

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: documentation

#19 - Create a Log2FC heatmap

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: enhancement

#18 - Cancer types are not well defined

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: enhancement

#17 - Find independent tumor/healthy data

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: enhancement

#16 - Extract metastatic samples

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: enhancement

#15 - Stratify the analysis with clinical variables

Issue - State: closed - Opened by MrHedmad over 1 year ago - 2 comments
Labels: enhancement

#14 - Redefine the metasplit calls to be more specific

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: enhancement

#13 - Make the MTP-DB release static

Issue - State: closed - Opened by MrHedmad over 1 year ago - 1 comment
Labels: enhancement

#12 - Use a better structure for the geneset graph

Issue - State: closed - Opened by MrHedmad over 1 year ago - 1 comment
Labels: enhancement, help wanted

#11 - No way to add custom genesets

Issue - State: closed - Opened by MrHedmad over 1 year ago - 1 comment
Labels: enhancement

#10 - Add extra data for verification

Issue - State: closed - Opened by MrHedmad over 1 year ago - 1 comment
Labels: enhancement

#9 - Using the t-statistic is not completely correct

Issue - State: closed - Opened by MrHedmad over 1 year ago
Labels: bug

#8 - Pre-preprint changes

Pull Request - State: closed - Opened by MrHedmad over 1 year ago - 1 comment

#7 - Update in the paper all the old CMA-Lab urls to the newest TCP-Lab equivalents

Issue - State: closed - Opened by Feat-FeAR over 1 year ago - 1 comment
Labels: bug

#6 - Using Xena directly may not be reproducible

Issue - State: closed - Opened by MrHedmad over 1 year ago - 1 comment

#5 - Adapt to the new MTP-DB

Pull Request - State: closed - Opened by MrHedmad over 1 year ago

#4 - To deseq

Pull Request - State: closed - Opened by MrHedmad over 1 year ago

#3 - Better to use DESeq2 for logFC calculation

Issue - State: closed - Opened by Feat-FeAR almost 2 years ago - 1 comment

#2 - Choen implementation

Pull Request - State: closed - Opened by MrHedmad almost 2 years ago

#1 - fgsea returns NAs when using cohen's D

Issue - State: closed - Opened by MrHedmad almost 2 years ago - 1 comment