Pinned Repositories
16S_pipeline
16S RNA microbiome pipeline
ATACseqQC
ATAC-seq Quality Control
ChIPpeakAnno
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline. Hyperlink is an example of output index page.
ChIPseqStepByStep
Integrated analysis and visualization of ChIP-seq data using ChIPpeakAnno, GeneNetworkBuilder and TrackViewer
MintChIP
pipeline for MintChIP
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
ribosomeProfilingQC
An R package for quality assessment of ribosome profiling
trackViewer
A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
trackViewer.documentation
documentation for trackViewer
jianhong's Repositories
jianhong/trackViewer
A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
jianhong/ATACseqQC
ATAC-seq Quality Control
jianhong/motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
jianhong/ChIPpeakAnno
jianhong/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline. Hyperlink is an example of output index page.
jianhong/ribosomeProfilingQC
An R package for quality assessment of ribosome profiling
jianhong/scRNAseqApp
single cell RNA-seq results report system
jianhong/HMMtBroadPeak
call broad peak by a modified Baum_Welch algorithm that supports multi-dimensional Student's t emission.
jianhong/GeneNetworkBuilder
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
jianhong/genomictools
docker file for genomic tools
jianhong/geomeTriD
A package for interactive 3D plot of epigenetic data
jianhong/hicar
This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
jianhong/NADfinder
Call wide peaks for sequencing data
jianhong/ATACseqTFEA
jianhong/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
jianhong/BEER
BEER: Batch EffEct Remover for single-cell data
jianhong/cdQuPath
Codex downstream analysis with QuPath
jianhong/cleanUpdTSeq
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
jianhong/codex_qupath
The script collection for qupath
jianhong/dagLogo
Visualize significant conserved amino acid sequence pattern in groups based on probability theory
jianhong/enhancerHomologSearch
Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog region for given sequences
jianhong/GenomicInteractionNodes
jianhong/hicar_doc
jianhong/hicVennDiagram
jianhong/InPAS
Identification of Novel alternative PolyAdenylation Sites (PAS)
jianhong/loopBouquetPlotDocumentation
The Documentation for loopBouquetPlot
jianhong/merip
jianhong/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
jianhong/ratte
The use of RnA-seq for AnnoTation of Transpose Elements
jianhong/scRNA-seq_notes
A list of scRNA-seq analysis tools