#

single-cell

Here are 639 public repositories matching this topic...

seandavi / awesome-single-cell

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

Updated Mar 11, 2023

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish 10x single-cell-rna-seq selective-alignment rna-seq-quantification

Updated Mar 12, 2023
C++

KrishnaswamyLab / PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

data-visualization dimensionality-reduction unsupervised-learning single-cell manifold-learning

Updated Mar 10, 2023
Python

scRNA-seq_notes

mdozmorov / scRNA-seq_notes

A list of scRNA-seq analysis tools

scrna-seq single-cell

Updated Feb 23, 2023
R

agitter / single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

bioinformatics rna-seq single-cell pseudotime-algorithms

Updated Mar 11, 2023

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.

transcription-factors transcriptomics single-cell gene-regulatory-network

Updated Nov 21, 2022
Python

welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets

r single-cell nonnegative-matrix-factorization

Updated Mar 10, 2023
HTML

flowhub-team / awesome-omics

A collection of awesome things regarding all omics.

awesome genomics ngs protein omics single-cell ngs-pipeline wgs-analysis

Updated Mar 22, 2022

luntergroup / octopus

Bayesian haplotype-based mutation calling

bioinformatics genomics somatic-variants haplotypes variants variant-calling single-cell phasing de-novo-mutation

Updated Jul 21, 2022
C++

scRNA-tools / scRNA-tools

Table of software for the analysis of single-cell RNA-seq data.

rna-seq database tools software scrna-seq single-cell single-cell-rna-seq

Updated Mar 13, 2023
R

theislab / scarches

Reference mapping for single-cell genomics

deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas

Updated Mar 9, 2023
Jupyter Notebook

milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

bioinformatics rna-seq sequencing immunology t-cell antibody t-cell-receptor rep-seq single-cell 10x

Updated Mar 13, 2023
Kotlin

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

rna-seq pipeline expression rnaseq umi single-cell fastq barcodes dge

Updated Mar 11, 2023
R

theislab / single-cell-best-practices

This project is work in progress! https://www.sc-best-practices.org

tutorial rna-seq book single-cell

Updated Mar 11, 2023
Jupyter Notebook

immunomind / immunarch

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Updated Feb 7, 2023
R

GLUE

gao-lab / GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

bioinformatics deep-learning single-cell single-cell-multiomics

Updated Aug 28, 2022
Python

stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data

bioinformatics single-cell atac

Updated Mar 10, 2023
R

iSEE / iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

visualization gui shiny clustering gene-expression feature-extraction transcriptomics single-cell hacktoberfest dimension-reduction human-cell-atlas

Updated Mar 10, 2023
R

OmicsML / dance

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

python data-science benchmark machine-learning bioinformatics deep-learning computational-biology dance single-cell multimodality single-cell-rna-seq graph-neural-networks spatial-transcriptomics single-cell-rna-sequencing

Updated Mar 12, 2023
Python

theislab / scgen

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq transcriptomics single-cell single-cell-genomics

Updated Feb 15, 2023
Python

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