hengbingao's repositories
ROSE
ROSE: RANK ORDERING OF SUPER-ENHANCERS
DeepTFni_single-cell-transcription-factors
A VGAE-based model to infer transcription factor regulatory network
SHARE-seq-alignment
pipeline for demultiplex and align both ATAC and RNA data generated in SHARE-seq
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
Irisas
Integrated region-based variants synchronization and Annotation for different inbreeding lines
BRAKER
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
seurat-wrappers
Community-provided extensions to Seurat
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
CNEFinder
CNEFinder: Finding Conserved Non-coding Elements in Genomes
TBtools
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
sex-gap-e0-pnas
Replication materials for
Circos-Pipeline
circos pipeline
MutMap
MutMap pipeline to identify causative mutations responsible for a phenotype
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
fishplot
Create timecourse "fish plots" that show changes in the clonal architecture of tumors
ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
RNA-seq
R to visualization
iSTARR-seq_data_analysis
computational code for iSTARR-seq paper
CNSpipeline
phast cons calculate
ggpointdensity
:chart_with_upwards_trend: :bar_chart: Introduces geom_pointdensity(): A Cross Between a Scatter Plot and a 2D Density Plot.
ngsTools
Programs to analyse NGS data for population genetics purposes
10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
Scripts
Ka_Ks calculator
circos
Maybe a circos image generator in c++