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Commit 1e6b007f authored by Anna Buschart's avatar Anna Buschart
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parent 99fbe60e
This repository contains code used in the multiomic analyses of faecal microbiota from four families with several cases of T1DM ( __MuSt__ ).
to build a search data base for [proteomics](proteomics-data-base.md) from predicted proteins and their variants:
rename4proteomics.pl
trypsinStartEnd.pl
variant_annotateRepairedTab.pl
variants_annotateTab4Stats.pl
variants_locateType.pl
⋅⋅* rename4proteomics.pl
⋅⋅* trypsinStartEnd.pl
⋅⋅* variant_annotateRepairedTab.pl
⋅⋅* variants_annotateTab4Stats.pl
⋅⋅* 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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