Pinned Repositories
extract-transcript-regions
For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and CDS).
haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
homer-idr
Applying IDR analysis to Homer peaks.
homerkit
Read HOMER motif analysis output in R.
MakeGencodeTSS
Makes distinct TSS of each gene from a Gencode annotation
networkD3
D3 JavaScript Network Graphs from R
NGSTools
Next-Generation Sequencing(NGS) toolkits.
nlpUtilityBelt
Auxiliary NLP tools
NucleoATAC
nucleosome calling using ATAC-seq
peaks-report
A quick report to make a plot & table of the number of peaks per BED file in a dir
Tools-jusuE404's Repositories
Tools-jusuE404/ATACPrimerTool
Primer design for ATAC-qPCR
Tools-jusuE404/BiFET
A robust statistical test for TF footprint data analyses
Tools-jusuE404/EnrichedHeatmap
make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
Tools-jusuE404/haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Tools-jusuE404/networkD3
D3 JavaScript Network Graphs from R
Tools-jusuE404/nlpUtilityBelt
Auxiliary NLP tools
Tools-jusuE404/NucleoATAC
nucleosome calling using ATAC-seq
Tools-jusuE404/NucleoATACR
R package for reading in & working with NucleoATAC outputs
Tools-jusuE404/PIQ
Tools-jusuE404/annotables
R data package for annotating/converting Gene IDs
Tools-jusuE404/AuPairWise
Tools-jusuE404/bam2tcc
Tools-jusuE404/bwtool
A tool for bigWig files.
Tools-jusuE404/ChIPseqSpikeInFree
A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
Tools-jusuE404/ChromHMM
Tools-jusuE404/chromVAR
chromatin Variability Across Regions (of the genome!)
Tools-jusuE404/circRNA_finder
Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).
Tools-jusuE404/ComplexHeatmap
make complex heatmaps as well as self define annotation graphics
Tools-jusuE404/ConsHMM
Tools-jusuE404/csvkit
A suite of utilities for converting to and working with CSV, the king of tabular file formats.
Tools-jusuE404/EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
Tools-jusuE404/fishermp
FisherMP: Motif Prediction using Fisher's exact test with openMP Parallel design
Tools-jusuE404/gat
Genomic Association Tester
Tools-jusuE404/genie
A quick way into a systemd "bottle" for WSL
Tools-jusuE404/gg3D
A ggplot2 extension enabling 3D projections
Tools-jusuE404/ggpubr
'ggplot2' Based Publication Ready Plots
Tools-jusuE404/piq-single
PIQ DNA footprinting. Cloned from https://bitbucket.org/thashim/piq-single
Tools-jusuE404/pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
Tools-jusuE404/RITAN
Rapid Integration of Term Annotation and Network resources
Tools-jusuE404/upload-client
Upload client for the ISMARA web-service (www.ismara.unibas.ch)