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 184
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 177
JEFworks-Lab / STalign
Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
alignment bioinformatics diffeomorphism singlecell spatialtranscriptomics
Language:HTML 88
aristoteleo / Scribe-py
Regulatory networks with Direct Information in python
rnaseq singlecell network causality velocity slam-seq
Language:Python 40
euxhenh / cellar
Interactive software tool for the assignment of cell types in single-cell studies.
python gui genomics genomics-visualization clustering singlecell sc-rna-seq sc-atac-seq codex spatial-transcriptomics
Language:Python 34
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
cell-atlas clustering leidenalg scrna-seq scrna-seq-analysis singlecell
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
OmicsSuite / OmicsSuite.github.io
OmicsSuite website for releasing new version.
bioinformatics genomics java javafx metabolomics multi-omics omicssuite singlecell software transcriptomics
Language:HTML 23
IMB-Computational-Genomics-Lab / ascend
R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
r rpackages scrna-seq-analysis scrnaseq singlecell
Language:R 22
biolab / orange3-single-cell
🍊🔬 Orange add-on for gene expression of single cell data
orange scorange singlecell
Language:Python 17
JinmiaoChenLab / DISCOtoolkit_py
Python version of DISCO toolkit
atlas-data rna-seq singlecell
Language:Python 13
dibbelab / singlecell_bcatlas
Breast Cancer Single Cell Atlas
breastcancer singlecell dropseq cell-lines gf-icf
12
luglilab / Cytophenograph
Pipeline for flow cytometry anlaysis
phenograph cytometry-analysis-pipeline singlecell python3 cytometry flowsom parc flowcytometry
Language:Python 8
BlueBrain / BluePyEModel
Blue Brain Python Electrical Modeling Pipeline
neuroscience python simulation modelling analyse build emodel neuron optimisation parameter singlecell visualise workflow
Language:Python 7
sjessa / cytoscope
A Shiny app for visualizing and exploring single cell RNA-sequencing data
singlecell single-cell scrna-seq visualization shiny
Language:R 7
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
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
autoencoder nmf singlecell 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
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 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
openbraininstitute / BluePyEModel
Blue Brain Python Electrical Modeling Pipeline
analyse build emodel modelling neuron neuroscience optimisation parameters python simulation singlecell workflow
Language:Python 2
aksarkar / poisbeta
Inference algorithms for the Poisson-Beta model
singlecell
Language:Python 1
aksarkar / singlecell-ideas
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
Irrationall / CellOrigin
Predicting cell fate with single cell data
mic singlecell cellfate relativedimension
Language:Python 1
Mengxicici / dinov2_For_GeoMX
single cell segmentation based on DINO-2 a vision transformer model, aim to analysis multiplex fluorescent imaging data
dinov2 geomx proteomics segmentation singlecell vision-transformer
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

singlecell

pinellolab / scATAC-benchmarking

pinellolab / STREAM

JEFworks-Lab / STalign

aristoteleo / Scribe-py

euxhenh / cellar

qiaochen / VeloAE

fabilab / northstar

debsin / dropClust

olgabot / cshl-singlecell-2017

OmicsSuite / OmicsSuite.github.io

IMB-Computational-Genomics-Lab / ascend

biolab / orange3-single-cell

JinmiaoChenLab / DISCOtoolkit_py

dibbelab / singlecell_bcatlas

luglilab / Cytophenograph

BlueBrain / BluePyEModel

sjessa / cytoscope

milescsmith / scRNAimputeR

aislyn / TCR_circos

aksarkar / scmodes

bixBeta / TReX

aksarkar / anmf

aksarkar / singlecell-modes

aristoteleo / Scribe-Python-notebooks

SkadiEye / RZiMM

ddiez / celltype

HHengUG / hatpal

openbraininstitute / BluePyEModel

aksarkar / poisbeta

aksarkar / singlecell-ideas

aristoteleo / Scribe

himelmallick / BenchmarkSingleCell

Irrationall / CellOrigin

Mengxicici / dinov2_For_GeoMX

merckey / scOh

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