Commit 751abe99 authored by Anna Buschart's avatar Anna Buschart
Browse files

README

parent c7d8c36f
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) from predicted proteins and their variants:
rename4proteomics.pl
trypsinStartEnd.pl
variant_annotateRepairedTab.pl
variants_annotateTab4Stats.pl
variants_locateType.pl
to parse [functional annotations](functional-annotations) of gene predictions (some including [coverage](calculating-coverage)):
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) of the best hit from the mOTU database:
fastaExtractWithCoordBase1.pl
getValidGenes1.R
getValidGenes2new.R
getHitPhylogenyNew.R
to parse taxonomy of [MG-RAST annotations](taxonomic-MG-RAST-annotations) of genes:
parse_taxbrowser_MGRAST.py
MGRASTgeneLevelTax.R
to automatically [cluster](automatic-clustering) contigs based on nucleotide signature (BH-SNE maps), DNA coverage and essential genes:
autoCluster.R
fastaExtractCutRibosomal1000.pl
makeWSvarAnnoCorrect.R
to [reconstruct](reconstructed-KO-network) a metabolic network from KOs and analyse it:
140630_MUST_NW.R
with file 150705_KOs_in_NW.tsv
runHeinz.sh
plotModules_omicLevels.R
to feed a [mongo database](mongo-database) 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
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