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10k_genomes

Various scripts for efficient processing of 10k Salmonella genomes

annogesic_scripts

running ANNOgesic for Salmonella

apredeus.github.io

NGS bioinformatics and pipelines

bioconda-recipes

Conda recipes for the bioconda channel.

d24359

data and scripts used to assemble and annotate S. Enteritidis strain D24359

d37_salmonella_paper

all the code and small data files relevant to D37712 genome + RNA-seq paper

ent_4str

guess_ensg

Series of scripts useful at guessing of used 10x or Ensembl/Gencode reference from a list of gene names

multi-bacpipe

A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

myodiff

Analysis and making of figures for C2C12 myodiff RNA-seq paper

old_genequery

Old stand-alone application and web-server for GeneQuery, as well as source code for binary files. Preprocessing is available elsewhere.

p_alcalifaciens

genome analysis of P. alcalifaciens

rnaquant

RNA-seq quantification pipeline for eukaryotic species

salmonella_pathways

Custom gene sets enriched in Salmonella under various in vitro and in vivo conditions

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

skater_rnaseq

Analysis of whole blood RNA-sequencing of skaters before and after exercise

tradis

In-house pipeline for processing of TIS/TRADIS data

yakutica

Analysis scripts for Gortzia yakutica paper