scverse/scanpy

Single-cell analysis in Python. Scales to >1M cells.

Language: Python - Size: 38.6 MB - Last synced: about 20 hours ago - Pushed: about 22 hours ago - Stars: 1,772 - Forks: 576

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.02 GB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 237 - Forks: 303

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.

Language: Python - Size: 34.7 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 380 - Forks: 175

scverse/anndata

Annotated data.

Language: Python - Size: 4.33 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 501 - Forks: 150

chanzuckerberg/cellxgene

An interactive explorer for single-cell transcriptomics data

Language: JavaScript - Size: 239 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 579 - Forks: 111

mahmoodlab/PathomicFusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

Language: Jupyter Notebook - Size: 42.4 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 222 - Forks: 71

hms-dbmi/scde

R package for analyzing single-cell RNA-seq data

Language: R - Size: 14 MB - Last synced: 30 days ago - Pushed: 3 months ago - Stars: 170 - Forks: 68

spacetx/starfish

starfish: unified pipelines for image-based transcriptomics

Language: Python - Size: 114 MB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 220 - Forks: 66

VerisimilitudeX/DNAnalyzer

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Language: Java - Size: 188 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 125 - Forks: 55

owkin/PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Language: Python - Size: 1.29 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 508 - Forks: 55

theislab/scgen

Single cell perturbation prediction

Language: Python - Size: 69 MB - Last synced: 18 days ago - Pushed: 8 months ago - Stars: 247 - Forks: 51

kharchenkolab/pagoda2

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

Language: JavaScript - Size: 78.4 MB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 191 - Forks: 47

obophenotype/cell-ontology

An ontology of cell types

Language: Makefile - Size: 316 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 130 - Forks: 47

iSEE/iSEE

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

Language: R - Size: 16.4 MB - Last synced: 6 days ago - Pushed: 14 days ago - Stars: 220 - Forks: 41

ZJUFanLab/scCATCH

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Language: R - Size: 52 MB - Last synced: 15 days ago - Pushed: about 1 year ago - Stars: 202 - Forks: 36

Novartis/cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

Language: Python - Size: 203 KB - Last synced: 15 days ago - Pushed: 2 months ago - Stars: 52 - Forks: 32

AllenInstitute/scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

Language: HTML - Size: 154 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 95 - Forks: 31

JEFworks-Lab/HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

Language: R - Size: 52.8 MB - Last synced: 5 days ago - Pushed: almost 3 years ago - Stars: 95 - Forks: 31

dib-lab/dammit

just annotate it, dammit!

Language: Python - Size: 12.1 MB - Last synced: 25 days ago - Pushed: 9 months ago - Stars: 87 - Forks: 28

emanuega/MERlin

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

Language: Python - Size: 16.2 MB - Last synced: 5 months ago - Pushed: over 2 years ago - Stars: 24 - Forks: 27

NathanSkene/EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Language: R - Size: 35.2 MB - Last synced: 14 days ago - Pushed: 16 days ago - Stars: 51 - Forks: 24

theislab/diffxpy

Differential expression analysis for single-cell RNA-seq data.

Language: Python - Size: 1.71 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 171 - Forks: 23

stemangiola/tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

Language: R - Size: 95.1 MB - Last synced: about 6 hours ago - Pushed: about 6 hours ago - Stars: 159 - Forks: 23

GoekeLab/sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Language: Jupyter Notebook - Size: 2.36 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 87 - Forks: 23

nanoporetech/pychopper 📦

A tool to identify, orient, trim and rescue full length cDNA reads

Language: Python - Size: 52 MB - Last synced: 7 days ago - Pushed: almost 2 years ago - Stars: 78 - Forks: 22

GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

Language: Python - Size: 4.96 MB - Last synced: 2 days ago - Pushed: 17 days ago - Stars: 127 - Forks: 22

quadbio/Pando

Multiome GRN inference.

Language: R - Size: 35.3 MB - Last synced: 3 days ago - Pushed: 27 days ago - Stars: 102 - Forks: 21

saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 68.9 MB - Last synced: about 4 hours ago - Pushed: 2 days ago - Stars: 139 - Forks: 20

genular/pandora

PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:

Language: Vue - Size: 16 MB - Last synced: 14 days ago - Pushed: 24 days ago - Stars: 133 - Forks: 20

GoekeLab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Language: R - Size: 637 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 118 - Forks: 19

arc85/celltalker

Inference of cell-cell communication from single-cell RNAseq data

Language: R - Size: 11.1 MB - Last synced: 3 months ago - Pushed: 11 months ago - Stars: 44 - Forks: 18

ZJUFanLab/scDeepSort

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

Language: Python - Size: 19.4 MB - Last synced: 4 days ago - Pushed: 10 months ago - Stars: 93 - Forks: 17

keller-mark/awesome-biological-visualizations

A list of web-based interactive biological data visualizations.

Size: 141 KB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 152 - Forks: 16

raw-lab/metaome_stats

Statistical package for metaome denovo assembly results.

Language: Python - Size: 2.64 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 2 - Forks: 16

saezlab/cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Language: R - Size: 45.1 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 52 - Forks: 15

COMBINE-lab/alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Language: Rust - Size: 4.08 MB - Last synced: 7 days ago - Pushed: 2 months ago - Stars: 152 - Forks: 15

urmi-21/MetaOmGraph

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Language: Java - Size: 175 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 32 - Forks: 14

PalMuc/TransPi

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Language: Nextflow - Size: 48.6 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 24 - Forks: 14

nanoporetech/pinfish 📦

Tools to annotate genomes using long read transcriptomics data

Language: Go - Size: 120 MB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 43 - Forks: 13

GuyTeichman/RNAlysis

RNA sequencing analysis software

Language: Python - Size: 613 MB - Last synced: about 9 hours ago - Pushed: about 22 hours ago - Stars: 121 - Forks: 13

nf-core/spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Language: Nextflow - Size: 6.94 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 39 - Forks: 12

JEFworks/MUDAN

Multi-sample Unified Discriminant ANalysis

Language: R - Size: 60.1 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 65 - Forks: 12

egaffo/CirComPara

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

Language: R - Size: 16 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 14 - Forks: 11

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 170 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 37 - Forks: 11

benben-miao/TOmicsVis

Transcriptomics Visualization R package.

Language: R - Size: 198 MB - Last synced: 6 days ago - Pushed: 4 months ago - Stars: 56 - Forks: 11

ablab/IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Language: Python - Size: 18.7 MB - Last synced: about 20 hours ago - Pushed: 1 day ago - Stars: 120 - Forks: 11

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced: 4 days ago - Pushed: 17 days ago - Stars: 64 - Forks: 10

sdomanskyi/DigitalCellSorter

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Language: Python - Size: 1020 MB - Last synced: 26 days ago - Pushed: almost 3 years ago - Stars: 22 - Forks: 10

DeplanckeLab/ASAP

ASAP : Automated Single-cell Analysis Pipeline

Language: Java - Size: 170 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 23 - Forks: 10

wenbostar/PGA

PGA: a tool for ProteoGenomics Analysis

Language: R - Size: 187 MB - Last synced: 5 months ago - Pushed: about 2 years ago - Stars: 6 - Forks: 10

NGSchoolEU/ngs17

Materials used during #NGSchool2017

Language: HTML - Size: 1.61 GB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 9 - Forks: 10

myles-lewis/glmmSeq

Gene-level general linear mixed model

Language: R - Size: 13.8 MB - Last synced: 13 days ago - Pushed: 9 months ago - Stars: 18 - Forks: 10

GuangyuWangLab2021/cellDancer

Predict RNA velocity through deep learning

Language: Jupyter Notebook - Size: 764 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 46 - Forks: 10

stemangiola/bioc_2020_tidytranscriptomics

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Language: R - Size: 48.5 MB - Last synced: 4 months ago - Pushed: over 3 years ago - Stars: 26 - Forks: 10

thelovelab/fishpond

Differential expression and allelic analysis, nonparametric statistics

Language: R - Size: 7.01 MB - Last synced: 8 days ago - Pushed: 9 months ago - Stars: 24 - Forks: 9

stasaki/DEcode

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Language: Jupyter Notebook - Size: 97.7 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 21 - Forks: 9

StatBiomed/UniTVelo

UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference

Language: Jupyter Notebook - Size: 20.2 MB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 22 - Forks: 9

PaccMann/paccmann_rl

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

Size: 31.3 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 29 - Forks: 9

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 115 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 27 - Forks: 8

collaborativebioinformatics/isocomp

Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq

Language: HTML - Size: 49 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 2 - Forks: 8

alexisvdb/singleCellHaystack

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Language: R - Size: 78.2 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 73 - Forks: 8

klarman-cell-observatory/scPlot

Single cell interactive plotting tools

Language: Jupyter Notebook - Size: 37.9 MB - Last synced: 7 days ago - Pushed: almost 4 years ago - Stars: 24 - Forks: 8

markziemann/dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Language: Shell - Size: 56 MB - Last synced: 7 days ago - Pushed: 9 months ago - Stars: 39 - Forks: 8

bpucker/teaching

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Size: 268 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 40 - Forks: 8

federicomarini/GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Language: R - Size: 115 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 75 - Forks: 8

KatrionaGoldmann/volcano3D

An R package to plot interactive three-way differential expression analysis

Language: HTML - Size: 219 MB - Last synced: 13 days ago - Pushed: 9 months ago - Stars: 31 - Forks: 7

Oshlack/MINTIE

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Language: Python - Size: 21.8 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 32 - Forks: 7

czbiohub-sf/tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

Language: Jupyter Notebook - Size: 788 MB - Last synced: 9 months ago - Pushed: 12 months ago - Stars: 30 - Forks: 7

OceanGenomics/mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates

Language: Rust - Size: 18.3 MB - Last synced: 11 days ago - Pushed: 9 months ago - Stars: 30 - Forks: 7

ajitjohnson/imsig

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

Language: R - Size: 285 KB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 24 - Forks: 7

orangeSi/GSSplayground

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

Language: HTML - Size: 148 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 27 - Forks: 7

nf-core/slamseq Fork of t-neumann/slamseq

SLAMSeq processing and analysis pipeline

Language: Nextflow - Size: 4.46 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 7

rajewsky-lab/openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Language: HTML - Size: 170 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 25 - Forks: 7

MannLabs/OmicLearn Fork of OmicEra/OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Language: Python - Size: 22.2 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 28 - Forks: 6

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.6 MB - Last synced: 16 days ago - Pushed: 20 days ago - Stars: 17 - Forks: 6

CCBR/MAAPster

MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data

Language: R - Size: 50.5 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 6

TBroTeam/TBro

Visualization and management of denovo transcriptomes

Language: PHP - Size: 268 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 10 - Forks: 6

pachterlab/voyager

From geospatial to spatial -omics

Language: R - Size: 4.1 GB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 60 - Forks: 6

my-rna-health/rna-seq

bioinformatics pipelines

Language: wdl - Size: 3.06 MB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 6

nanoporetech/pipeline-nanopore-denovo-isoforms 📦

Pipeline for de novo clustering of long transcriptomic reads

Language: Python - Size: 27.2 MB - Last synced: 7 days ago - Pushed: over 2 years ago - Stars: 26 - Forks: 6

wukevin/rnagps

Interpretable model of sub-cellular RNA localization.

Language: Jupyter Notebook - Size: 481 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 6

MatthiasLienhard/isotools

IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis.

Language: Jupyter Notebook - Size: 38 MB - Last synced: 7 days ago - Pushed: 7 months ago - Stars: 19 - Forks: 5

lcalviell/Ribo-seQC

A comprehensive analysis tool for Ribo-seq and small RNA-seq data

Language: HTML - Size: 16.1 MB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 8 - Forks: 5

zavolanlab/zarp

The Zavolab Automated RNA-seq Pipeline

Language: Python - Size: 23.8 MB - Last synced: 28 days ago - Pushed: 2 months ago - Stars: 28 - Forks: 5

cansysbio/HGSOC_TME_Heterogeneity

Analysis of treatment naive and neo-adjuvant chemotherapy treated high-grade serous ovarian cancer samples

Language: Jupyter Notebook - Size: 132 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 5

3inar/nowaclean

NOWAC data cleaning package

Language: R - Size: 1.67 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 5

ocbe-uio/DIscBIO

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

Language: Jupyter Notebook - Size: 230 MB - Last synced: 6 days ago - Pushed: 6 months ago - Stars: 11 - Forks: 5

pwatrick/DrugRepurposingToolKit

Language: R - Size: 5.51 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 5

nanoporetech/pipeline-pinfish-analysis 📦

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Language: Python - Size: 137 KB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 27 - Forks: 5

pinellolab/pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

Language: Python - Size: 21.8 MB - Last synced: 6 days ago - Pushed: 16 days ago - Stars: 35 - Forks: 5

ipw012/RIVER

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Language: R - Size: 2.79 MB - Last synced: 4 months ago - Pushed: about 4 years ago - Stars: 10 - Forks: 4

sepro/LSTrAP 📦

Language: Python - Size: 33.4 MB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 8 - Forks: 4

guigolab/LyRic

Long RNA-seq analysis workflow

Language: Python - Size: 664 KB - Last synced: about 6 hours ago - Pushed: about 19 hours ago - Stars: 10 - Forks: 4

BgeeDB/bgee_pipeline

Source code of the Bgee pipeline used to build the Bgee database

Language: Perl - Size: 1020 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 11 - Forks: 4

Bayer-Group/cellenium

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

Language: Jupyter Notebook - Size: 12.4 MB - Last synced: 29 days ago - Pushed: 6 months ago - Stars: 23 - Forks: 4

CarineRey/caars

CAARS: Comparative Assembly and Annotation of RNA-Seq data

Language: Python - Size: 19.9 MB - Last synced: 9 months ago - Pushed: almost 4 years ago - Stars: 8 - Forks: 4

enriquea/feseR

feseR: Combining feature selection methods for analyzing omics data

Language: R - Size: 172 MB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 14 - Forks: 4

PavlidisLab/rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Language: Python - Size: 43.5 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 19 - Forks: 4

vpc-ccg/circminer

A sensitive and fast tool for circular RNA detection from RNA-Seq data

Language: C++ - Size: 1.27 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 9 - Forks: 4

glasgowcompbio/pyMultiOmics

Python toolbox for multi-omics data mapping and analysis

Language: Jupyter Notebook - Size: 45.9 MB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 15 - Forks: 4