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Code for the manuscript "Machine learning reveals STAT motifs as predictors for GR-mediated gene repression"
TODO: Add citation once paper is accepted
Software dependencies
BSgenome.Mmusculus.UCSC.mm10
BSgenome.Mmusculus.UCSC.mm9
org.Mm.eg.db
TxDb.Mmusculus.UCSC.mm10.knownGene
macs2
biomaRt
universalmotif
BEDTools
Bowtie 2
CAGEr
ChIPpeakAnno
ChIPseeker
ComplexHeatmap
Consensus
Cutadapt
DeepTools
DESeq2
FastQC
FiMO
genomation
GenomicRanges
MEME
memes
MultiQC
Picard
plyranges
rtracklayer
SAMtools
Snakemake
topGO
circlize
data.table
dplyr
ggplot2
ggpubr
glmnet
here
optparse
plsgenomics
plyr
png
RColorBrewer
stringr
Hypermutated Tumor Mutational Signature Detection and Visualization Pipeline
This pipeline is designed to detect and visualise Mutational Signatures in Hypermutated Tumors Designed and Edited by : Moham...
A mini snakemake pipeline to batch construct consensus sequences from long nanopore amplicons w/ medaka for a set of samples
A mini snakemake pipeline for batch constructing consensus sequences from long nanopore amplicons with medaka for a set of sa...
Genomics - Recombination and selection analysis
This workflow employs a recombination detection algorithm (GARD) developed by Kosakovsky Pond et al. and implemented in the h...
This workflow performs an RNA-seq analysis from the sequencing output data to the differential expression analyses.
Thomas Vannier (@metavannier), https://centuri-livingsystems.org/t-vannier/ This workflow performs an RNA-seq analysis from t...
Variant Allele Frequency Lookup from gnomAD using RocksDB
Fast look up interface allel frequency of variants from gnomad with rocksdb.
conda install -c conda-forge python-rocksdb
pip ...
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