Repository navigation
Add test dataset for wormcat - #2356
Open
DanHUMassMed wants to merge 1 commit into
Open
DanHUMassMed wants to merge 1 commit into
DanHUMassMed wants to merge 1 commit into
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds Caenorhabditis elegans test datasets under
data/genomics/eukaryotes/caenorhabditis_elegans/for testing thewormcatmoduleThe module will be submitted after the test data is accepted.
wormcat3provide gene category enrichment functionality and can be reviewed at (http://test.wormcat.com)followed guidance from slack conversation with Matthias Hörtenhuber
Added Files
data/genomics/eukaryotes/caenorhabditis_elegans/background_gene_sets/test_detected.csv: Background set of detected WormBase gene IDs (WBGene*).data/genomics/eukaryotes/caenorhabditis_elegans/differential_expression/deseq2_results.csv: Subset of DESeq2 differential expression results for C. elegans.data/genomics/eukaryotes/caenorhabditis_elegans/gene_annotations/test_annotaions.csv: WormCat gene category annotation mapping (Sequence ID,Wormbase ID,Category 1–3).data/genomics/eukaryotes/caenorhabditis_elegans/gene_lists/test_down.csv: Single-column CSV list of downregulated WormBase gene IDs for enrichment testing.data/genomics/eukaryotes/caenorhabditis_elegans/gene_lists/test_genes.xlsx: Multi-sheet Excel workbook of gene lists for testing Excel input support inwormcat2.