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10x-scatac-2019

Publication Page for Satpathy*, Granja* et al 2019

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

atac-seq

Analysis pipeline for ATAC-seq data

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

brain-enhancer

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

cellspace

Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace

circos

Maybe a circos image generator in c++

circos-pipeline

circos pipeline

cisdynet_bulkatac_rnaseq

An integrated platform for modeling gene-regulatory dynamics and networks

cnefinder

CNEFinder: Finding Conserved Non-coding Elements in Genomes

cnmf_elif_removebatch

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

cnspipeline

phast cons calculate

cpgtools

Python package to analyze DNA methylation data

deeptfni_single-cell-transcription-factors

A VGAE-based model to infer transcription factor regulatory network

edta

Extensive de-novo TE Annotator

episcanpy-

fast_calculate_unsigned_tom_from_unsigned_or_signed_adjacency_matrix_of_wgcna

Optimize weighted gene co-expression network analysis (WGCNA, a R package): fast calculate unsigned Topological Overlap Matrix from unsigned or signed Adjacency Matrix

fastqc

csf fork of fastqc for usage on selected reads of unaligned bam file

find_cns

find conserved non-coding sequences (CNS)

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

fusion_twas

methods for functional summary-based imputation

genie3

GENIE3 (GEne Network Inference with Ensemble of trees) R-package

gggenomes

A grammar of graphics for comparative genomics

ggpointdensity

:chart_with_upwards_trend: :bar_chart: Introduces geom_pointdensity(): A Cross Between a Scatter Plot and a 2D Density Plot.

glue_tools

Graph-linked unified embedding for single-cell multi-omics data integration

gwas_grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

irisas

Integrated region-based variants synchronization and Annotation for different inbreeding lines

istarr-seq_data_analysis

computational code for iSTARR-seq paper