transcriptomics
There are 574 repositories under transcriptomics topic.
scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
pachterlab/gget
🧬 gget enables efficient querying of genomic reference databases
chanzuckerberg/cellxgene
An interactive explorer for single-cell transcriptomics data
owkin/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
scverse/anndata
Annotated data.
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.
mahmoodlab/PathomicFusion
Fusing Histology and Genomics via Deep Learning - IEEE TMI
theislab/scgen
Single cell perturbation prediction
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
spacetx/starfish
starfish: unified pipelines for image-based transcriptomics
kharchenkolab/pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
ZJUFanLab/scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
iSEE/iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
GoekeLab/bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
keller-mark/awesome-biological-visualizations
A list of web-based interactive biological data visualizations.
theislab/diffxpy
Differential expression analysis for single-cell RNA-seq data.
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.
saezlab/decoupler-py
Python package to perform enrichment analysis from omics data.
obophenotype/cell-ontology
An ontology of cell types
ablab/IsoQuant
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
hms-dbmi/scde
R package for analyzing single-cell RNA-seq data
stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
VerisimilitudeX/DNAnalyzer
Precision genomics for everyone, everywhere. Powered by private AI.
GoekeLab/xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing
genular/pandora
PANDORA :computer:
GuyTeichman/RNAlysis
Analyze your RNA sequencing data without writing a single line of code
GoekeLab/sg-nex-data
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
quadbio/Pando
Multiome GRN inference.
AllenInstitute/scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
rajewsky-lab/openst
Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
ZJUFanLab/scDeepSort
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
JEFworks-Lab/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
pachterlab/voyager
From geospatial to spatial -omics
dib-lab/dammit
just annotate it, dammit!
alexisvdb/singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
nanoporetech/pychopper
A tool to identify, orient, trim and rescue full length cDNA reads