singlecell

There are 0 repository under singlecell topic.

pinellolab / scATAC-benchmarking
Benchmarking computational single cell ATAC-seq methods
atac-seq bash benchmark jupyternotebook python r reproducible singlecell
Language:Jupyter Notebook 177
pinellolab / STREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
singlecell trajectory lineage visualization scatac-seq scrna-seq python
Language:Jupyter Notebook 173
JEFworks-Lab / STalign
Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
singlecell spatialtranscriptomics diffeomorphism alignment bioinformatics
Language:HTML 69
aristoteleo / Scribe-py
Regulatory networks with Direct Information in python
rnaseq singlecell network causality velocity slam-seq
Language:Python 38
euxhenh / cellar
Interactive software tool for the assignment of cell types in single-cell studies.
clustering codex genomics genomics-visualization gui python sc-atac-seq sc-rna-seq singlecell spatial-transcriptomics
Language:Python 32
qiaochen / VeloAE
Low-dimensional Projection of Single Cell Velocity
autoencoder velocity singlecell
Language:Jupyter Notebook 28
fabilab / northstar
Single cell type annotation guided by cell atlases, with freedom to be queer
singlecell cell-atlas leidenalg clustering scrna-seq scrna-seq-analysis
Language:Python 25
debsin / dropClust
Version 2.1.0 released
cluster-analysis clustering genomics lsh-forest pca rna-seq singlecell
Language:R 23
olgabot / cshl-singlecell-2017
Single Cell Analysis course at Cold Spring Harbor Laboratory 2017
singlecell single-cell bioinformatics machinelearning pca tsne scikit-learn matplotlib seaborn python jupyter-notebook
Language:Jupyter Notebook 23
IMB-Computational-Genomics-Lab / ascend
R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
scrna-seq-analysis scrnaseq r rpackages singlecell
Language:R 22
OmicsSuite / OmicsSuite.github.io
OmicsSuite website for releasing new version.
bioinformatics genomics java javafx metabolomics multi-omics omicssuite singlecell software transcriptomics
Language:HTML 18
biolab / orange3-single-cell
🍊🔬 Orange add-on for gene expression of single cell data
orange scorange singlecell
Language:Python 17
dibbelab / singlecell_bcatlas
Breast Cancer Single Cell Atlas
breastcancer singlecell dropseq cell-lines gf-icf
11
JinmiaoChenLab / DISCOtoolkit_py
Python version of DISCO toolkit
atlas-data rna-seq singlecell
Language:Python 11
sjessa / cytoscope
A Shiny app for visualizing and exploring single cell RNA-sequencing data
singlecell single-cell scrna-seq visualization shiny
Language:R 7
BlueBrain / BluePyEModel
Blue Brain Python Electrical Modeling Pipeline
neuroscience python simulation modelling analyse build emodel neuron optimisation parameter singlecell visualise workflow
Language:Python 6
milescsmith / scRNAimputeR
A effort to collect all of the scRNA imputation methods and allow them to interface with scRNA-seq libraries (i. e. Seurat, SingleCellAssay, etc...)
scrna-imputation-methods seurat singlecell single-cell-analysis scrna-seq s
Language:R 6
luglilab / Cytophenograph
Pipeline for flow cytometry anlaysis
phenograph cytometry-analysis-pipeline singlecell python3 cytometry flowsom parc flowcytometry
Language:Python 5
aislyn / TCR_circos
R function to generate a circos-style ggplot from single-cell TCR data.
tcr singlecell circos ggplot2 plot immunogenomics
Language:R 4
aksarkar / scmodes
singlecell
Language:Python 4
bixBeta / TReX
RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @Cornell-Trex
10xgenomics rnaseq singlecell scrna shiny-apps shiny bash-script bash-scripting smallrna-seq smallrna mirdeep2 star seurat multiqc ggplot2
Language:Shell 4
aksarkar / anmf
Amortized NMF
singlecell autoencoder nmf vae
Language:Python 3
aksarkar / singlecell-modes
singlecell benchmark
Language:Python 3
aristoteleo / Scribe-Python-notebooks
Tutorials of Scribe Python package usage cases
rnaseq singlecell network causality velocity slam-seq
Language:Jupyter Notebook 3
ddiez / celltype
An R package for cell type prediction from single cell omics data
bioinformatics single-cell singlecell
Language:R 2
HHengUG / hatpal
hatpal is an R package for alternative polyadenylation (APA) identification & analysis using 3’ scRNA-seq (10x etc.).
bioinformatics polyadenylation scrna-seq singlecell
Language:R 2
SkadiEye / RZiMM
RZiMM: A Regularized Zero-inflated Mixture Model for scRNA-seq Data
singlecell clustering differentially-expressed-genes batch-effects zero-inflated dropout scrna-seq
Language:R 2
aksarkar / poisbeta
Inference algorithms for the Poisson-Beta model
singlecell
Language:Python 1
aristoteleo / Scribe
Regulatory networks with Direct Information
singlecell rna-seq causality network velocity direct-information
Language:C++ 1
himelmallick / BenchmarkSingleCell
Large-scale Benchmarking of Single-cell Differential Expression Analysis Methods
singlecell differential-expression benchmarking scrna-seq scrna-seq-analysis scrna-seq-data differential-analysis
Language:R 1
merckey / scOh
Single Cell Atlas - PDAC
pdac singlecell
Language:HTML 1
merckey / Single-cell-multi-omic-profiling-of-glioblastoma-associated-myeloid-cells
Single-cell multi-omic profiling of glioblastoma-associated myeloid cells
gbm omics singlecell
Language:R 1
aksarkar / singlecell-ideas
singlecell
Language:Python 0
Cadaei-Yuvxvs / snRNAseq_muscle_MND
Single Nuclei RNA Sequencing analysis of MND muscle cultures for the paper "Impaired signaling for neuromuscular synaptic maintenance is a feature of Motor Neuron Disease" by Ding et al, published in Acta Neuropathologica Communications.
mnd r research research-paper single-cell single-nuclei single-nuclei-rna-sequencing muscle scrna-seq singlecell cell
Language:R 0
genepattern / Conos.VisualizeGeneExpression
Visualize expression of genes of interest after Conos.Cluster has been ran.
genepattern-module singlecell single-cell
Language:R
SydneyBioX / iDAS
Interpretable Differential Abundance signature
differential-abundance differential-expression idas singlecell
Language:R

singlecell

pinellolab / scATAC-benchmarking

pinellolab / STREAM

JEFworks-Lab / STalign

aristoteleo / Scribe-py

euxhenh / cellar

qiaochen / VeloAE

fabilab / northstar

debsin / dropClust

olgabot / cshl-singlecell-2017

IMB-Computational-Genomics-Lab / ascend

OmicsSuite / OmicsSuite.github.io

biolab / orange3-single-cell

dibbelab / singlecell_bcatlas

JinmiaoChenLab / DISCOtoolkit_py

sjessa / cytoscope

BlueBrain / BluePyEModel

milescsmith / scRNAimputeR

luglilab / Cytophenograph

aislyn / TCR_circos

aksarkar / scmodes

bixBeta / TReX

aksarkar / anmf

aksarkar / singlecell-modes

aristoteleo / Scribe-Python-notebooks

ddiez / celltype

HHengUG / hatpal

SkadiEye / RZiMM

aksarkar / poisbeta

aristoteleo / Scribe

himelmallick / BenchmarkSingleCell

merckey / scOh

merckey / Single-cell-multi-omic-profiling-of-glioblastoma-associated-myeloid-cells

aksarkar / singlecell-ideas

Cadaei-Yuvxvs / snRNAseq_muscle_MND

genepattern / Conos.VisualizeGeneExpression

SydneyBioX / iDAS