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chipseeker

:dart:ChIP peak Annotation, Comparison and Visualization

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

cms

Composite of Multiple Signals: tests for selection in meiotically recombinant populations

co-occurrence_network_analysis

R and python scripts for correlation-based network analysis

cornet

Correlation networks with R

corrplot

Package corrplot is for visualizing a correlation matrix

crassphage_project

Source code for the crAssphage project

ctlmapping

Correlated Trait Locus (CTL) mapping

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

goshifter

GoShifter

gseama

Gene Set Enrichment Analysis Made Awesome

gseapy

Gene Set Enrichment Analysis in Python

ldsc

LD Score Regression (LDSC)

locuscomparer

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

locusexplorer

An interactive graphical illustration of genetic associations and their biological context

microbial-interkingdom-suppl

Scripts and tables for Duran & Thiergart et al. 2018 (unpublished)

multigsea

A unified interface to a plethora of gene set enrichment analysis methods

multigsea.shiny

Provides shiny components to visualize multilGSEA results

my_wgcna

netmeta

Official Git repository of R package netmeta

network

randomize correlation matrix for Networks FDR estimation

nkx2-5_ase_ipsc-cm

Notebooks and scripts for the paper : Allele-Specific NKX2-5 Binding Underlies Multiple Genetic Associations with Human Electrocardiographic Traits

rlowpc

R function to construct Relevance Low order Partial Correlation gene networks

rnaseq_pipeline

Pipeline of somatic variant analysis using Waldenstrom macroglobulinemia patient’s RNA-seq data, including tools like STAR, HTseq, VarScan in parallel computing in SGE clusters, Deseq2 and GSEA in R

scikit-mdr

A sklearn-compatible Python implementation of Multifactor Dimensionality Reduction (MDR) for feature construction.

seurat

R toolkit for single cell genomics

ssgsea2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

tcga_example

visualizernaseq

R scripts used for visualization of RNA-seq data