transcriptomics

There are 36 repositories under transcriptomics topic.

scanpy
scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
machine-learning data-science visualize-data transcriptomics bioinformatics scanpy anndata python scverse
Language:Python 2248
gget
pachterlab / gget
🧬 gget enables efficient querying of genomic reference databases
alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl genomics gget ncbi proteomics reference rna-seq transcriptomics uniprot
Language:Python 1071
instadeepai / nucleotide-transformer
Foundation Models for Genomics & Transcriptomics
genomics deep-learning transformer dna foundation-models transcriptomics biology
Language:Jupyter Notebook 725
chanzuckerberg / cellxgene
An interactive explorer for single-cell transcriptomics data
dataviz scientific scrna-seq transcriptomics visualization
Language:JavaScript 712
owkin / PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
bioinformatics differential-expression python rna-seq transcriptomics
Language:Python 695
scverse / anndata
Annotated data.
scanpy data-science transcriptomics bioinformatics machine-learning scverse anndata
Language:Python 681
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.
single-cell transcriptomics gene-regulatory-network transcription-factors
Language:Python 553
mahmoodlab / PathomicFusion
Fusing Histology and Genomics via Deep Learning - IEEE TMI
pathomic fusion multimodal pathology histopathology transcriptomics genomics multimodal-network computational-pathogenomics mahmoodlab
Language:Jupyter Notebook 324
theislab / scgen
Single cell perturbation prediction
transcriptomics deep-learning generative-model bioinformatics single-cell scrna-seq single-cell-genomics
Language:Python 323
opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra-toolbox reconstruction tutorial metabolic-models metabolic-reconstruction metabolic-engineering gap-filling strain-engineering omics-data-integration metabolomics transcriptomics cobra constraint-based-modeling human-metabolism microbiome-analysis
Language:MATLAB 269
spacetx / starfish
starfish: unified pipelines for image-based transcriptomics
transcriptomics imaging human-cell-atlas python
Language:Python 244
kharchenkolab / pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
single-cell transcriptomics scrna-seq single-cell-rna-seq
Language:JavaScript 239
scverse / decoupler
Python package to perform enrichment analysis from omics data.
python data-science bioinformatics transcriptomics numba single-cell spatial-transcriptomics enrichment enrichment-analysis
Language:Python 236
ZJUFanLab / scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
marker-genes cell-markers cluster-annotation seurat single-cell rna-seq transcriptomics sequencing transcriptome
Language:R 234
iSEE / iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
visualization gui dimension-reduction feature-extraction clustering transcriptomics single-cell gene-expression shiny human-cell-atlas hacktoberfest
Language:R 228
bambu
GoekeLab / bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
bambu transcript-reconstruction transcript-quantification long-reads nanopore-sequencing transcriptomics rna-seq-analysis bioconductor r nanopore rna-seq
Language:R 222
keller-mark / awesome-biological-visualizations
A list of web-based interactive biological data visualizations.
awesome awesome-list biology cancer data-visualization genomics medicine transcriptomics visualization
209
theislab / diffxpy
Differential expression analysis for single-cell RNA-seq data.
differential-expression single-cell-rna-seq gene-set-enrichment bioinformatics transcriptomics tensorflow
Language:Python 204
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.
10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics
Language:Rust 194
ablab / IsoQuant
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
ngs transcriptomics pacbio nanopore bioinformatics rna-seq
Language:Python 192
cell-ontology
obophenotype / cell-ontology
An ontology of cell types
obofoundry cell-ontology ontology anatomy cell-types owl anatomy-ontology semantic-web genomics transcriptomics metazoa monarchinitiative
Language:Makefile 184
hms-dbmi / scde
R package for analyzing single-cell RNA-seq data
bioinformatics single-cell transcriptomics heterogenity analysis r ngs
Language:R 176
tidybulk
stemangiola / tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
tidyverse tidy tidy-data bioconductor edger deseq2 transcriptomics pipe tibble gene-symbols bulk-transcriptional-analyses mds-dimensions ensembl-ids transcripts tsne pca redundancy entrez gsea differential-expression
Language:R 173
xpore
GoekeLab / xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing
rna modification transcriptomics machine-learning genomics nanopore-sequencing rna-seq rna-modifications nanopore python
Language:Python 158
sg-nex-data
GoekeLab / sg-nex-data
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
direct-rna-sequencing long-reads nanopore rna-seq transcriptomics
Language:R 143
RNAlysis
GuyTeichman / RNAlysis
Analyze your RNA sequencing data without writing a single line of code
rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna smallrna-seq gui-application
Language:Python 139
genular / pandora
PANDORA :computer:
machine-learning systems-biology data-science data-visualization data-mining pandora bioinformatics biomarkers clinical-data clustering data-integration drug-discovery genomic-data-analysis microbiome predictive-analytics transcriptomics tsne umap unsupervised-machine-learning
Language:Vue 138
quadbio / Pando
Multiome GRN inference.
single-cell transcriptomics epigenomics
Language:R 127
AllenInstitute / scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
clustering jaccard r transcriptomics wgcna
Language:HTML 115
rajewsky-lab / openst
Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
bioinformatics omics spatial-transcriptomics transcriptomics
Language:HTML 106
ZJUFanLab / scDeepSort
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
annotation cell-type-classification deep-learning gnn graph-neural-network reference-free scrna-seq single-cell transcriptomics
Language:Python 106
JEFworks-Lab / HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
single-cell-analysis single-cell-rna-seq cnv-detection transcriptomics subpopulation hmm bayesian heterogeneity bioinformatics
Language:R 98
pachterlab / voyager
From geospatial to spatial -omics
bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics
Language:R 98
dib-lab / dammit
just annotate it, dammit!
annotation transcriptomics bioinformatics
Language:Python 93
lilab-bcb / cirrocumulus
Bring your single-cell data to life
scrna-seq visualization single-cell anndata bioinformatics transcriptomics webgl scanpy seurat spatial 10x smartseq2 data-visualization
Language:JavaScript 88
alexisvdb / singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
bioinformatics single-cell r transcriptomics spatial-transcriptomics cite-seq pseudotime scatac-seq spatial-proteomics
Language:R 85