Tools-jusuE404's repositories
ATACPrimerTool
Primer design for ATAC-qPCR
BiFET
A robust statistical test for TF footprint data analyses
EnrichedHeatmap
make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
networkD3
D3 JavaScript Network Graphs from R
NucleoATACR
R package for reading in & working with NucleoATAC outputs
annotables
R data package for annotating/converting Gene IDs
bwtool
A tool for bigWig files.
ChIPseqSpikeInFree
A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
chromVAR
chromatin Variability Across Regions (of the genome!)
circRNA_finder
Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).
ComplexHeatmap
make complex heatmaps as well as self define annotation graphics
csvkit
A suite of utilities for converting to and working with CSV, the king of tabular file formats.
EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
fishermp
FisherMP: Motif Prediction using Fisher's exact test with openMP Parallel design
gat
Genomic Association Tester
genie
A quick way into a systemd "bottle" for WSL
gg3D
A ggplot2 extension enabling 3D projections
ggpubr
'ggplot2' Based Publication Ready Plots
nlpUtilityBelt
Auxiliary NLP tools
NucleoATAC
nucleosome calling using ATAC-seq
piq-single
PIQ DNA footprinting. Cloned from https://bitbucket.org/thashim/piq-single
pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
RITAN
Rapid Integration of Term Annotation and Network resources
upload-client
Upload client for the ISMARA web-service (www.ismara.unibas.ch)