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Commit 07a1e424 authored by Anna Buschart's avatar Anna Buschart
Browse files

links in readme, part2

parent 42fc6dc9
......@@ -14,41 +14,41 @@ to parse [functional annotations](functional-annotations.md) of gene predictions
* [consolidate_hmmscan_results.pl](consolidate_hmmscan_results.pl)
* [consolidate_hmmscan_results_justKEGG.pl](consolidate_hmmscan_results_justKEGG.pl)
* [150705_MUST_keggParseNW.py](150705_MUST_keggParseNW.py)
* [ko2des_clean.txt](ko2des_clean.txt)
* ko2des_clean.txt - pretty big text [file](ko2des_clean.txt)
* [calculateCoverageAndGaps2.pl](calculateCoverageAndGaps2.pl)
* [150322_bestHmmReadParse.py](150322_bestHmmReadParse.py)
* [150415_bestHmmAveCovParse.py](150415_bestHmmAveCovParse.py)
* [150630_keggReadParse.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](fastaExtractWithCoordBase1.pl)
* [getValidGenes1.R](getValidGenes1.R)
* [getValidGenes2new.R](getValidGenes2new.R)
* [getHitPhylogenyNew.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](parse_taxbrowser_MGRAST.py)
* [MGRASTgeneLevelTax.R](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](autoCluster.R)
* [fastaExtractCutRibosomal1000.pl](fastaExtractCutRibosomal1000.pl)
* [makeWSvarAnnoCorrect.R](makeWSvarAnnoCorrect.R)
to gather contig clusters by [related phylogenetic marker genes in a phylogenetic tree](phylogenetic-marker-genes-trees.md):
* 150819_MUST_tree.R
* [150819_MUST_tree.R](150819_MUST_tree.R)
to [reconstruct](reconstructed-KO-network.md) a metabolic network from KOs and analyse it:
* [140630_MUST_NW.R](140630_MUST_NW.R)
* with file 150705_KOs_in_NW.tsv
* runHeinz.sh
* plotModules_omicLevels.R
* the above script needs [file](150705_KOs_in_NW.tsv) 150705_KOs_in_NW.tsv
* [runHeinz.sh](runHeinz.sh)
* [plotModules_omicLevels.R](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](150928_mongifyMust.py)
* [151020_funOIMongoWS.R](151020_funOIMongoWS.R)
* [150928_MUST_relatedClusterWSFromMongo.R](150928_MUST_relatedClusterWSFromMongo.R)
* [eukaryoticGenesMongo.R](eukaryoticGenesMongo.R)
* [virusGenesMongo.R](virusGenesMongo.R)
* [getNWexprMongoAllSamples.R](getNWexprMongoAllSamples.R)
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