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Commit 9f744c28 authored by Anna Buschart's avatar Anna Buschart
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edit README

parent 5efd5dbf
......@@ -8,44 +8,44 @@ to build a search data base for [proteomics](proteomics-data-base.md) from predi
* variants_locateType.pl
to parse [functional annotations](functional-annotations.md) of gene predictions (some including [coverage](calculating-coverage.md)):
⋅⋅* 150310_MUST_hmmBestAll.py
⋅⋅* 150705_MUST_hmmParse.py
⋅⋅* 150705_MUST_hmmParsePfam.py
⋅⋅* consolidate_hmmscan_results.pl
⋅⋅* consolidate_hmmscan_results_justKEGG.pl
⋅⋅* 150705_MUST_keggParseNW.py
⋅⋅* ko2des_clean.txt
⋅⋅* calculateCoverageAndGaps2.pl
⋅⋅* 150322_bestHmmReadParse.py
⋅⋅* 150415_bestHmmAveCovParse.py
⋅⋅* 150630_keggReadParse.py
* 150310_MUST_hmmBestAll.py
* 150705_MUST_hmmParse.py
* 150705_MUST_hmmParsePfam.py
* consolidate_hmmscan_results.pl
* consolidate_hmmscan_results_justKEGG.pl
* 150705_MUST_keggParseNW.py
* ko2des_clean.txt
* calculateCoverageAndGaps2.pl
* 150322_bestHmmReadParse.py
* 150415_bestHmmAveCovParse.py
* 150630_keggReadParse.py
to annotate phylogenetic [marker genes with the taxonomy](annotate-phylogenetic-marker-genes.md) of the best hit from the mOTU database:
⋅⋅* fastaExtractWithCoordBase1.pl
⋅⋅* getValidGenes1.R
⋅⋅* getValidGenes2new.R
⋅⋅* getHitPhylogenyNew.R
* fastaExtractWithCoordBase1.pl
* getValidGenes1.R
* getValidGenes2new.R
* getHitPhylogenyNew.R
to parse taxonomy of [MG-RAST annotations](taxonomic-MG-RAST-annotations.md) of genes:
⋅⋅* parse_taxbrowser_MGRAST.py
⋅⋅* MGRASTgeneLevelTax.R
* parse_taxbrowser_MGRAST.py
* MGRASTgeneLevelTax.R
to automatically [cluster](automatic-clustering.md) contigs based on nucleotide signature (BH-SNE maps), DNA coverage and essential genes:
⋅⋅* autoCluster.R
⋅⋅* fastaExtractCutRibosomal1000.pl
⋅⋅* makeWSvarAnnoCorrect.R
* autoCluster.R
* fastaExtractCutRibosomal1000.pl
* makeWSvarAnnoCorrect.R
to [reconstruct](reconstructed-KO-network.md) a metabolic network from KOs and analyse it:
⋅⋅* 140630_MUST_NW.R
⋅⋅* with file 150705_KOs_in_NW.tsv
⋅⋅* runHeinz.sh
⋅⋅* plotModules_omicLevels.R
* 140630_MUST_NW.R
* with file 150705_KOs_in_NW.tsv
* runHeinz.sh
* plotModules_omicLevels.R
to feed a [mongo database](mongo-database.md) with all the data from MuSt and retrieve some of the data:
⋅⋅* 150928_mongifyMust.py
⋅⋅* 151020_funOIMongoWS.R
⋅⋅* 150928_MUST_relatedClusterWSFromMongo.R
⋅⋅* eukaryoticGenesMongo.R
⋅⋅* virusGenesMongo.R
⋅⋅* getNWexprMongoAllSamples.R
* 150928_mongifyMust.py
* 151020_funOIMongoWS.R
* 150928_MUST_relatedClusterWSFromMongo.R
* eukaryoticGenesMongo.R
* virusGenesMongo.R
* getNWexprMongoAllSamples.R
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