ElliotXie/CASSIA

CASSIA: A multiagent llm based single cell Annottaion framework

Language: Python - Size: 258 MB - Last synced at: about 19 hours ago - Pushed at: about 19 hours ago - Stars: 32 - Forks: 2

openbraininstitute/BluePyEModel

Blue Brain Python Electrical Modeling Pipeline

Language: Python - Size: 38.1 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 1

SydneyBioX/iDAS

Interpretable Differential Abundance signature

Language: R - Size: 11.5 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

BlueBrain/BluePyEModel 📦

Blue Brain Python Electrical Modeling Pipeline

Language: Python - Size: 53.2 MB - Last synced at: about 17 hours ago - Pushed at: 3 months ago - Stars: 7 - Forks: 7

Irrationall/CellOrigin

Predicting cell fate with single cell data

Language: Python - Size: 75.2 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

pinellolab/scATAC-benchmarking

Benchmarking computational single cell ATAC-seq methods

Language: Jupyter Notebook - Size: 1.34 GB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 182 - Forks: 40

mpckkk/scChatBot

Personal Single Cell ChatBot

Language: Python - Size: 33.2 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

JinmiaoChenLab/DISCOtoolkit_py

Python version of DISCO toolkit

Language: Python - Size: 108 MB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 13 - Forks: 1

IMB-Computational-Genomics-Lab/ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

Language: R - Size: 256 MB - Last synced at: about 1 month ago - Pushed at: over 5 years ago - Stars: 22 - Forks: 7

biolab/orange3-single-cell

🍊🔬 Orange add-on for gene expression of single cell data

Language: Python - Size: 134 MB - Last synced at: 25 days ago - Pushed at: 11 months ago - Stars: 17 - Forks: 25

OmicsSuite/OmicsSuite.github.io

OmicsSuite website for releasing new version.

Language: HTML - Size: 14.9 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 19 - Forks: 2

euxhenh/cellar

Interactive software tool for the assignment of cell types in single-cell studies.

Language: Python - Size: 51.9 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 31 - Forks: 7

fabilab/northstar

Single cell type annotation guided by cell atlases, with freedom to be queer

Language: Python - Size: 304 KB - Last synced at: 12 days ago - Pushed at: almost 3 years ago - Stars: 25 - Forks: 6

pinellolab/STREAM

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

Language: Jupyter Notebook - Size: 249 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 170 - Forks: 47

aristoteleo/Scribe-Python-notebooks

Tutorials of Scribe Python package usage cases

Language: Jupyter Notebook - Size: 1.28 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 2

debsin/dropClust

Version 2.1.0 released

Language: R - Size: 188 MB - Last synced at: about 1 month ago - Pushed at: over 5 years ago - Stars: 23 - Forks: 8

qiaochen/VeloAE

Low-dimensional Projection of Single Cell Velocity

Language: Jupyter Notebook - Size: 990 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 1

JEFworks-Lab/STalign

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

Language: HTML - Size: 676 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 29 - Forks: 3

sjessa/cytoscope

A Shiny app for visualizing and exploring single cell RNA-sequencing data

Language: R - Size: 769 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 6 - Forks: 1

olgabot/cshl-singlecell-2017

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

Language: Jupyter Notebook - Size: 254 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 22 - Forks: 18

luglilab/Cytophenograph

Pipeline for flow cytometry anlaysis

Language: Python - Size: 363 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

dibbelab/singlecell_bcatlas

Breast Cancer Single Cell Atlas

Size: 2.57 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 4

aislyn/TCR_circos

R function to generate a circos-style ggplot from single-cell TCR data.

Language: R - Size: 218 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 0

aristoteleo/Scribe-py

Regulatory networks with Direct Information in python

Language: Python - Size: 242 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 36 - Forks: 6

SkadiEye/RZiMM

RZiMM: A Regularized Zero-inflated Mixture Model for scRNA-seq Data

Language: R - Size: 5.18 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

aksarkar/poisbeta

Inference algorithms for the Poisson-Beta model

Language: Python - Size: 7.81 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

aksarkar/singlecell-modes

Language: Python - Size: 90.5 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 2

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.

Language: R - Size: 2.56 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

genepattern/Conos.VisualizeGeneExpression

Visualize expression of genes of interest after Conos.Cluster has been ran.

Language: R - Size: 31.2 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

aksarkar/anmf

Amortized NMF

Language: Python - Size: 9.77 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

himelmallick/BenchmarkSingleCell

Large-scale Benchmarking of Single-cell Differential Expression Analysis Methods

Language: R - Size: 16.9 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

bixBeta/TReX

RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @Cornell-Trex

Language: Shell - Size: 1.06 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1

aksarkar/singlecell-ideas

Language: Python - Size: 20.3 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

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...)

Language: R - Size: 73.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

aksarkar/scmodes

Language: Python - Size: 210 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 0

HHengUG/hatpal

hatpal is an R package for alternative polyadenylation (APA) identification & analysis using 3’ scRNA-seq (10x etc.).

Language: R - Size: 63.5 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0

ddiez/celltype

An R package for cell type prediction from single cell omics data

Language: R - Size: 707 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 1

csawye01/nf-core-demultiplex

Demultiplexing pipeline for sequencing data

Language: Nextflow - Size: 367 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

aristoteleo/Scribe Fork of cole-trapnell-lab/Scribe

Regulatory networks with Direct Information

Language: C++ - Size: 195 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0