Pinned Repositories
3DChromatin_ReplicateQC
Software to compute reproducibility and quality scores for Hi-C data
analysis_SHOGUN
Analysis scripts and code for reproducing the analysis for the SHOGUN paper
ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
bioinfo-combio
The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/
biomarker-identification
This repository is the author implementation of the paper "Biomarker Identification by Reversing the Learning Mechanism of Autoencoder and Recursive Feature Elimination"
Bis-tools
A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )
biscuit
BISulfite-seq CUI Toolkit
bwa-meth
fast and accurate alignment of BS-Seq reads
Mmint
Versatile integrative analysis of DNA methylation, ChIP-seq and RNAseq
lijiacd985's Repositories
lijiacd985/Mmint
Versatile integrative analysis of DNA methylation, ChIP-seq and RNAseq
lijiacd985/ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
lijiacd985/bioinfo-combio
The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/
lijiacd985/biomarker-identification
This repository is the author implementation of the paper "Biomarker Identification by Reversing the Learning Mechanism of Autoencoder and Recursive Feature Elimination"
lijiacd985/biscuit
BISulfite-seq CUI Toolkit
lijiacd985/CaMelia
imputation in single-cell methylomes
lijiacd985/cfChIP-seek
cell-free ChIP-seq pipeline
lijiacd985/cfChIP-seq
Code to accompany publication on cell free chromatin immunoprecipitation (cfChIP)
lijiacd985/cfchip_manuscript
lijiacd985/cooler
A cool place to store your Hi-C
lijiacd985/cpg-transformer
CpG Transformer for imputation of single-cell methylomes
lijiacd985/epiScanpy
Episcanpy: Epigenomics Single Cell Analysis in Python
lijiacd985/granulator
lijiacd985/HaMiP
HaMiP: DNA hydroxymethylation analysis of Cytosine-5-methylenesulfonate ImmunoPrecipitation sequencing
lijiacd985/HiC_data
A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
lijiacd985/HiC_tools
A collection of tools for Hi-C data analysis
lijiacd985/inspectro
Hi-C spectral analysis workflow
lijiacd985/meth_atlas
lijiacd985/mustache
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
lijiacd985/RIMA
lijiacd985/scvelo
RNA Velocity generalized through dynamical modeling
lijiacd985/SEACR
SEACR: Sparse Enrichment Analysis for CUT&RUN
lijiacd985/Seurat.utils
Various utility functions for Seurat v3
lijiacd985/SpatialDecon
lijiacd985/TCGAsurvival
Scripts to analyze TCGA data
lijiacd985/TCR-BCR-seq-analysis
T/B cell receptor sequencing analysis notes
lijiacd985/velocyto-loom-bug
velocyto generated loom file did not count chrM, but chrMT. https://github.com/velocyto-team/velocyto.py/issues/318
lijiacd985/visium_heart
Spatial transcriptomics of heart tissue
lijiacd985/wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
lijiacd985/WisecondorX
WisecondorX — An evolved WISECONDOR