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Commit 0d8d359d authored by Anna Buschart's avatar Anna Buschart
Browse files

Readme improved

parent c29996d9
This repository contains code used in the multiomic analyses of faecal microbiota from four families with several cases of T1DM ( __MuSt__ ).
## This repository contains code used in the multiomic analyses of faecal microbiota from four families with several cases of T1DM ( __MuSt__ ).
You can find the different scripts behind the links next to the bullet points below. The links in the sub-headings below lead to descriptions of the workflows which connect the different scripts.
to build a search data base for [proteomics](proteomics-data-base.md) from predicted proteins and their variants:
### to build a search data base for [proteomics](proteomics-data-base.md) from predicted proteins and their variants:
* [rename4proteomics.pl](rename4proteomics.pl)
* [trypsinStartEndProdigal.pl](trypsinStartEndProdigal.pl) (corrected version)
* [variant_annotateRepairedTabProdigal.pl](variant_annotateRepairedTabProdigal.pl) (corrected version)
......@@ -11,7 +12,7 @@ to build a search data base for [proteomics](proteomics-data-base.md) from predi
* [variants_annotateTab4Stats.pl](variants_annotateTab4Stats.pl) (old version)
* [variants_locateType.pl](variants_locateType.pl)
to parse [functional annotations](functional-annotations.md) of gene predictions (some including [coverage](calculating-coverage.md)):
### to parse [functional annotations](functional-annotations.md) of gene predictions (some including [coverage](calculating-coverage.md)):
* [150310_MUST_hmmBestAll.py](150310_MUST_hmmBestAll.py)
* [150705_MUST_hmmParse.py](150705_MUST_hmmParse.py)
* [150705_MUST_hmmParsePfam.py](150705_MUST_hmmParsePfam.py)
......@@ -24,32 +25,32 @@ to parse [functional annotations](functional-annotations.md) of gene predictions
* [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:
### to annotate phylogenetic [marker genes with the taxonomy](annotate-phylogenetic-marker-genes.md) of the best hit from the mOTU database:
* [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:
### to parse taxonomy of [MG-RAST annotations](taxonomic-MG-RAST-annotations.md) of genes:
* [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:
### to automatically [cluster](automatic-clustering.md) contigs based on nucleotide signature (BH-SNE maps), DNA coverage and essential genes:
* [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):
### 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)
* [150816_getPhyloMarkers.R](150816_getPhyloMarkers.R)
to [reconstruct](reconstructed-KO-network.md) a metabolic network from KOs and analyse it:
### to [reconstruct](reconstructed-KO-network.md) a metabolic network from KOs and analyse it:
* [140630_MUST_NW.R](140630_MUST_NW.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:
### to feed a [mongo database](mongo-database.md) with all the data from MuSt and retrieve some of the data:
* [150928_mongifyMust.py](150928_mongifyMust.py)
* [151020_funOIMongoWS.R](151020_funOIMongoWS.R)
* [150928_MUST_relatedClusterWSFromMongo.R](150928_MUST_relatedClusterWSFromMongo.R)
......
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