yongjieliu

yongjieliu's Stars

• coder/code-server

  VS Code in the browser

  Language:TypeScript67.4k7243.5k5.5k

• seandavi/awesome-single-cell

  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

  3.1k25223960

• harvardinformatics/learning-bioinformatics-at-home

  resources for learning bioinformatics

  757432142

• mdozmorov/HiC_tools

  A collection of tools for Hi-C data analysis

  529356121

• meteostat/meteostat-python

  Access and analyze historical weather and climate data with Python.

  Language:Python40898659

• aertslab/SCENIC

  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

  Language:HTML4072229995

• chris-mcginnis-ucsf/DoubletFinder

  R package for detecting doublets in single-cell RNA sequencing data

  Language:R3938194105

• Starlitnightly/omicverse

  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

  Language:Jupyter Notebook39059945

• zhanghao-njmu/SCP

  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

  Language:R352812079

• stuart-lab/signac

  R toolkit for the analysis of single-cell chromatin data

  Language:R31561.2k85

• velocyto-team/velocyto.py

  RNA velocity estimation in Python

  Language:Python1581337082

• dynverse/dynmethods

  A collection of 50+ trajectory inference methods within a common interface 📥📤

  Language:R1181010526

• wu-yc/scMetabolism

  Quantifying metabolism activity at the single-cell resolution

  Language:R10853241

• Swarbricklab-code/BrCa_cell_atlas

  Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

  Language:R10263045

• jhkorhonen/MOODS

  MOODS: Motif Occurrence Detection Suite

  Language:C++9674312

• rnakato/ShortCake

  A docker image for single-cell analysis

  Language:R635713

• ay-lab/mustache

  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

  Language:Python6056211

• 4dn-dcic/docker-4dn-hic

  Docker for 4DN Hi-C processing pipeline

  Language:Common Workflow Language558417

• kundajelab/3DChromatin_ReplicateQC

  Software to compute reproducibility and quality scores for Hi-C data

  Language:Python4381816

• kundajelab/alzheimers_parkinsons

  Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

  Language:Jupyter Notebook4311215

• cboix/EPIMAP_ANALYSIS

  Epimap processing and analysis code repository

  Language:Jupyter Notebook332414

• broadinstitute/2019_scWorkshop

  Repo for Physalia course Analysis of Single Cell RNA-Seq data

  Language:TeX318018

• JinLabBioinfo/HiCorr

  HiCorr: a Hi-C data bias-correction pipeline

  Language:Perl27497

• higlass/higlass-manage

  A utility script to manage local docker instances of HiGlass

  Language:Python215709

• GenomicsNX/IKAP

  IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis

  Language:R1731110

• blmoore/mandelbrot

  Mandelbrot set R package

  Language:R9345

• drewvoigt10/cellcuratoR

  sharing interactive single cell gene expression visualizations from Seurat

  Language:R8393

• tanaylab/schic2

  Language:R8422

• tanaylab/shaman

  The shaman package - sampling HiC contact matrices for a-parametric normalization

  Language:R5451

• ChristopherBarrington/domainClassifyR

  Classification of TAD structures

  Language:R3110