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scrna-seq

Here are 236 public repositories matching this topic...

scverse / scvi-tools

Deep probabilistic analysis of single-cell omics data

deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse

Updated Mar 21, 2022
Python

hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course

r course sequencing bookdown scrna-seq scrna-seq-analysis

Updated Aug 10, 2021
TeX

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 15, 2022
C++

chanzuckerberg / cellxgene

An interactive explorer for single-cell transcriptomics data

visualization dataviz scrna-seq scientific transcriptomics

Updated Mar 12, 2022
JavaScript

immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

algorithm r scrna-seq data-integration

Updated Oct 29, 2021
R

scRNA-seq_notes

mdozmorov / scRNA-seq_notes

A list of scRNA-seq analysis tools

scrna-seq single-cell

Updated Mar 16, 2022
R

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 22, 2022
R

aristoteleo / dynamo-release

Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

dynamo scrna-seq differential-geometry dynamical-systems vector-field scslam-seq potential-landscape nasc-seq sci-fate scnt-seq rna-velocity cell-fate rna-jacobian rna-acceleration rna-curvature rna-divergence

Updated Mar 21, 2022
Python

liulab-dfci / MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline

transcription-factors epigenetics scrna-seq snakemake-workflows scatac-seq gene-regulatory-networks

Updated Jul 26, 2021
C

splatter

Oshlack / splatter

Simple simulation of single-cell RNA sequencing data

bioinformatics simulation bioconductor scrna-seq

Updated Mar 11, 2022
R

kharchenkolab / conos

R package for the joint analysis of multiple single-cell RNA-seq datasets

scrna-seq single-cell-rna-seq batch-correction

Updated Feb 5, 2022
R

pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

visualization python scrna-seq lineage trajectory singlecell scatac-seq

Updated Dec 18, 2021
Jupyter Notebook

kharchenkolab / pagoda2

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

scrna-seq transcriptomics single-cell single-cell-rna-seq

Updated Mar 15, 2022
JavaScript

dpeerlab / Palantir

Single cell trajectory detection

markov-chain dimensionality-reduction scrna-seq trajectory-generation diffusion-maps differentiation manifold-learning single-cell-genomics cell-fate-transitions scrna-seq-analysis

Updated Dec 15, 2021
Jupyter Notebook

rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

clustering dropout batch-normalization imputation scrna-seq diffusion-maps clustering-algorithm 3d umap normalization 10xgenomics cell-type-classification intractive-graph cite-seq singel-cell-sequencing pseudotime scvdj-seq icellr

Updated Mar 21, 2022
R

scverse / muon

Open

Plotting function should document parameters better

gtca commented Feb 16, 2022

As discussed in #49, documentation should be more clear that mu.pl.* support arguments from corresponding sc.pl.* functions.

Read more

enhancement good first issue

broadinstitute / Tangram

Spatial alignment of single cell transcriptomic data.

computational-biology gene-expression scrna-seq spatial-data visium snrna-seq

Updated Jan 22, 2022
Jupyter Notebook

wheaton5 / souporcell

Clustering scRNAseq by genotypes

bioinformatics genomics computational-biology scrna-seq scrnaseq scrna-seq-analysis

Updated Mar 19, 2021
Python

catavallejos / BASiCS

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

r rcpp gene-expression scrna-seq bayesian single-cell rcpparmadillo bioconductor-package

Updated Mar 16, 2022
R

eleozzr / desc

Deep Embedding for Single-cell Clustering

deep-learning clustering scrna-seq desc batch-remove

Updated Jul 31, 2020
Jupyter Notebook

kharchenkolab / dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

pipeline scrna-seq preprocessing single-cell-rna-seq

Updated Sep 27, 2020
C++

pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

scrna-seq kallisto single-cell-rna-seq rna-velocity-estimation bustools kb-python

Updated Mar 7, 2022
Python

dynverse / dynverse

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

benchmarking scrna-seq single-cell single-cell-rna-seq single-cell-omics trajectory-inference-methods

Updated May 20, 2021
R

JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.

Updated Mar 12, 2022
Jupyter Notebook

ZJUFanLab / scDeepSort

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

deep-learning annotation scrna-seq transcriptomics single-cell cell-type-classification gnn graph-neural-network reference-free

Updated Sep 10, 2021
Python

interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

visualization svg scrna-seq publication-quality-plots seurat scanpy cellxgene cellxgene-vip

Updated Feb 16, 2022
HTML

theislab / zellkonverter

Conversion between scRNA-seq objects

r conversion bioconductor scrna-seq

Updated Mar 21, 2022
R

czbiohub / cerebra

A tool for fast and accurate summarizing of variant calling format (VCF) files

genomics mutations scrna-seq variant-calling

Updated Sep 9, 2021
Python

simslab / scHPF

Single-cell Hierarchical Poisson Factorization

dimensionality-reduction scrna-seq variational-bayes

Updated Nov 9, 2020
Python

immunogenomics / symphony

Efficient and precise single-cell reference atlas mapping with Symphony

r mapping scrna-seq bioinfo

Updated Mar 15, 2022
R

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