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This repository contains code used in the multiomic analyses of faecal microbiota from four families with several cases of T1DM ( __MuSt__ ).

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to build a search data base for [proteomics](proteomics-data-base.md) from predicted proteins and their variants:
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⋅⋅* rename4proteomics.pl
⋅⋅* trypsinStartEnd.pl
⋅⋅* variant_annotateRepairedTab.pl
⋅⋅* variants_annotateTab4Stats.pl
⋅⋅* variants_locateType.pl
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to parse [functional annotations](functional-annotations.md) of gene predictions (some including [coverage](calculating-coverage.md)):
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⋅⋅* 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
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to annotate phylogenetic [marker genes with the taxonomy](annotate-phylogenetic-marker-genes.md) of the best hit from the mOTU database:
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⋅⋅* fastaExtractWithCoordBase1.pl
⋅⋅* getValidGenes1.R
⋅⋅* getValidGenes2new.R
⋅⋅* getHitPhylogenyNew.R
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to parse taxonomy of [MG-RAST annotations](taxonomic-MG-RAST-annotations.md) of genes:
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⋅⋅* parse_taxbrowser_MGRAST.py
⋅⋅* MGRASTgeneLevelTax.R
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to automatically [cluster](automatic-clustering.md) contigs based on nucleotide signature (BH-SNE maps), DNA coverage and essential genes:
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⋅⋅* autoCluster.R
⋅⋅* fastaExtractCutRibosomal1000.pl
⋅⋅* makeWSvarAnnoCorrect.R
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to [reconstruct](reconstructed-KO-network.md) a metabolic network from KOs and analyse it:
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⋅⋅* 140630_MUST_NW.R
⋅⋅* with file 150705_KOs_in_NW.tsv
⋅⋅* runHeinz.sh
⋅⋅* plotModules_omicLevels.R
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to feed a [mongo database](mongo-database.md) with all the data from MuSt and retrieve some of the data:
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⋅⋅* 150928_mongifyMust.py
⋅⋅* 151020_funOIMongoWS.R
⋅⋅* 150928_MUST_relatedClusterWSFromMongo.R
⋅⋅* eukaryoticGenesMongo.R
⋅⋅* virusGenesMongo.R
⋅⋅* getNWexprMongoAllSamples.R
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