lucygarner

lucygarner's Stars

• seandavi/awesome-single-cell

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

  3.2k24823974

• hms-dbmi/UpSetR

  An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

  Language:R75538233153

• mdozmorov/scRNA-seq_notes

  A list of scRNA-seq analysis tools

  Language:R620281144

• aertslab/pySCENIC

  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

  Language:Python42518532179

• dmcable/spacexr

  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

  Language:HTML296919272

• graphia-app/graphia

  A visualisation tool for the creation and analysis of graphs

  Language:C++23385120

• kharchenkolab/pagoda2

  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

  Language:JavaScript2041811447

• rcastelo/GSVA

  Gene set variation analysis

  Language:R1981011840

• BiomedicalMachineLearning/stLearn

  A novel machine learning pipeline to analyse spatial transcriptomics data

  Language:Python191616625

• compbiomed/singleCellTK

  Interactively analyze single cell genomic data

  Language:R1751413077

• saezlab/decoupler-py

  Python package to perform enrichment analysis from omics data.

  Language:Python158712623

• YosefLab/VISION

  Signature Analysis and Visualization for Single-Cell RNA-seq

  Language:R15469030

• NVIDIA-Genomics-Research/AtacWorks

  Deep learning based processing of Atac-seq data

  Language:Jupyter Notebook128810923

• aertslab/AUCell

  AUCell: score single cells with gene regulatory networks

  Language:R122104426

• zktuong/dandelion

  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data

  Language:Jupyter Notebook103913025

• saezlab/progeny

  R package for Pathway RespOnsive GENe activity inference

  Language:R93184819

• mdozmorov/scATAC-seq_notes

  scATAC-seq data analysis tools and papers

  913218

• Durenlab/LINGER

  7553214

• carmonalab/GeneNMF

  Methods to discover gene programs on single-cell data

  Language:R712123

• broadinstitute/2020_scWorkshop

  Code and data repository for the 2020 physalia course on single cell RNA sequencing.

  Language:Shell5510339

• NathanSkene/EWCE

  Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

  Language:R5358525

• willtownes/scrna2019

  supporting code for the multinomial single cell RNA-Seq paper

  Language:R515412

• guokai8/scGSVA

  scGSVA: Perform GSVA for single cell RNA seq

  Language:R452263

• heiniglab/scPower

  Experimental design framework for scRNAseq population studies (eQTL and DE)

  Language:R442235

• powellgenomicslab/DropletQC

  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

  Language:R326123

• WCSCourses/SingleCell_23

  Hands-on training on the latest methodologies and applications for the analysis of nucleic acids from eukaryotic single cells

  16403

• Drinchai/BloodGen3Module

  This R package for performing module repertoire analyses and generating fingerprint representations

  Language:R14385

• kdzimm/hierarchicell

  An R package for simulating cell-type specific and hierarchical single-cell expression data

  Language:R9396

• Taylor-CCB-Group/SpOOx

  SPatial Omics Oxford Analysis Pipeline

  Language:Python6781

• GabrielHoffman/crumblr

  Count ratio uncertainty modeling base linear regression

  Language:R4301