https://github.com/scverse/scanpy

Single-cell analysis in Python. Scales to >100M cells.

anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data

Last synced: 11 May 2025

https://github.com/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

Last synced: 14 May 2025

https://github.com/chanzuckerberg/cellxgene

An interactive explorer for single-cell transcriptomics data

dataviz scientific scrna-seq transcriptomics visualization

Last synced: 14 May 2025

https://github.com/owkin/PyDESeq2

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

bioinformatics differential-expression python rna-seq transcriptomics

Last synced: 09 May 2025

https://github.com/scverse/anndata

Annotated data.

anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics

Last synced: 29 Jan 2026

https://github.com/theislab/scgen

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq single-cell single-cell-genomics transcriptomics

Last synced: 11 Oct 2025

https://github.com/mahmoodlab/pathomicfusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

computational-pathogenomics fusion genomics histopathology mahmoodlab multimodal multimodal-network pathology pathomic transcriptomics

Last synced: 06 Apr 2025

https://github.com/isee/isee

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

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Last synced: 20 Oct 2025

https://github.com/iSEE/iSEE

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

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Last synced: 30 Jul 2025

https://github.com/GoekeLab/bambu

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

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 06 May 2025

https://github.com/saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

bioinformatics data-science enrichment enrichment-analysis numba python single-cell spatial-transcriptomics transcriptomics

Last synced: 15 May 2025

https://github.com/goekelab/bambu

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

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 15 May 2025

https://github.com/hms-dbmi/scde

R package for analyzing single-cell RNA-seq data

analysis bioinformatics heterogenity ngs r single-cell transcriptomics

Last synced: 09 Apr 2025

https://github.com/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

Last synced: 28 Apr 2025

https://github.com/goekelab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

genomics machine-learning modification nanopore nanopore-sequencing python rna rna-modifications rna-seq transcriptomics

Last synced: 16 May 2025

https://github.com/GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

genomics machine-learning modification nanopore nanopore-sequencing python rna rna-modifications rna-seq transcriptomics

Last synced: 06 May 2025

https://github.com/obophenotype/cell-ontology

An ontology of cell types

anatomy anatomy-ontology cell-ontology cell-types genomics metazoa monarchinitiative obofoundry ontology owl semantic-web transcriptomics

Last synced: 11 Mar 2025

https://github.com/genular/pandora

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

bioinformatics biomarkers clinical-data clustering data-integration data-mining data-science data-visualization drug-discovery genomic-data-analysis machine-learning microbiome pandora predictive-analytics systems-biology transcriptomics tsne umap unsupervised-machine-learning

Last synced: 03 Apr 2025

https://github.com/alleninstitute/scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

clustering jaccard r transcriptomics wgcna

Last synced: 12 Apr 2025

https://github.com/goekelab/sg-nex-data

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

direct-rna-sequencing long-reads nanopore rna-seq transcriptomics

Last synced: 05 Apr 2025

https://github.com/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

Last synced: 21 Jul 2025

https://github.com/JEFworks-Lab/HoneyBADGER

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

bayesian bioinformatics cnv-detection heterogeneity hmm single-cell-analysis single-cell-rna-seq subpopulation transcriptomics

Last synced: 09 Apr 2025

https://github.com/dib-lab/dammit

just annotate it, dammit!

annotation bioinformatics transcriptomics

Last synced: 19 Jan 2026

https://github.com/federicomarini/genetonic

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

bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression gui pathway-analysis r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome transcriptomics user-friendly

Last synced: 13 Apr 2025

https://github.com/pachterlab/voyager

From geospatial to spatial -omics

bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics

Last synced: 10 Apr 2025

https://github.com/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.

dataviz h5ad rna-seq scientific scrna-seq transcriptomics visualization

Last synced: 21 Jul 2025

https://github.com/saezlab/cosmosr

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

data-integration metabolomic-data network-modelling phosphoproteomics proteomics transcriptomics

Last synced: 09 Apr 2025

https://github.com/nathanskene/ewce

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

deconvolution single-cell single-cell-rna-seq transcriptomics

Last synced: 13 Apr 2025

https://github.com/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.

dataviz h5ad rna-seq scientific scrna-seq transcriptomics visualization

Last synced: 28 Sep 2025

https://github.com/theislab/drvi

Unsupervised Deep Disentangled Representation of Single-Cell Omics

anndata bioinformatics disentanglement integration python single-cell transcriptomics

Last synced: 11 Oct 2025

https://github.com/arc85/celltalker

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

ligands receptors single-cell transcriptomics

Last synced: 30 Apr 2025

https://github.com/pinellolab/pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming pyro rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-multiomics single-cell-rna-seq transcriptomics

Last synced: 06 Oct 2025

https://github.com/czbiohub-sf/tabula-sapiens

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

cell-atlas cell-ontologies human-anatomy sapiens single-cell-rna-seq transcriptomics

Last synced: 16 Jan 2026

https://github.com/alleninstitute/scrattch

Single cell RNA-seq analysis for transcriptomic type characterization

r scrattch transcriptomics umbrella

Last synced: 11 Apr 2025

https://github.com/zavolanlab/zarp

The Zavolab Automated RNA-seq Pipeline

bioinformatics conda docker fair high-throughput pipeline reproducible-research rna-seq singularity snakemake transcriptomics workflow

Last synced: 16 Jan 2026

https://github.com/dohlee/chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

artificial-intelligence bioinformatics deep-learning epigenomics gene-expression genomics histone-modifications transcriptomics transformer

Last synced: 29 Apr 2025

https://github.com/paccmann/paccmann_rl

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

de-novo-drug-design deep-learning drug-discovery drug-sensitivity generative-models transcriptomics

Last synced: 28 Mar 2025

https://github.com/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

bam bioinformatics comparative-genomics crosslink depth genecluster genome-viewer genomes igv-like indel long-reads read-mapping snp structure-variation sv svg synteny transcriptomics vcf visualization

Last synced: 18 Nov 2025

https://github.com/Novartis/pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics

Last synced: 28 Sep 2025

https://github.com/microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

ecoinformatics fair-data genomics linkml metabolomics metadata microbiome microbiomedata mixs nmdc proteomics samples schema standards transcriptomics

Last synced: 06 Apr 2025

https://github.com/novartis/pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics

Last synced: 21 Jul 2025

https://github.com/bayer-group/cellenium

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

bioinformatics dataviz scrna-seq transcriptomics

Last synced: 12 Apr 2025

https://github.com/Bayer-Group/cellenium

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

bioinformatics dataviz scrna-seq transcriptomics

Last synced: 28 Sep 2025

https://github.com/tidyomics/tidysummarizedexperiment

Brings SummarizedExperiment to the tidyverse

bioconductor genomics rnaseq summarizedexperiment tidyverse transcriptomics

Last synced: 11 Dec 2025

https://github.com/alleninstitute/scrattch.vis

scRNA-seq data visualization from scrattch

data-visualization r scrattch transcriptomics

Last synced: 11 Apr 2025

https://github.com/myles-lewis/glmmseq

Gene-level general linear mixed model

bioinformatics cran differential-gene-expression gene-expression glmm mixed-models transcriptomics

Last synced: 22 Oct 2025

https://github.com/lieberinstitute/spatialdlpfc

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

bioconductor dlpfc rstats spatial-transcriptomics spatialdlpfc transcriptomics visium visium-spg

Last synced: 31 Jan 2026

https://github.com/sydney-informatics-hub/bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling

Last synced: 16 Aug 2025

https://github.com/blengerich/personalized_regression

Personalized Regression

genomics linear-regression logistic-regression personalization personalized-regression rna-seq-analysis transcriptomics

Last synced: 16 Jun 2025

https://github.com/cran-task-views/omics

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

cran genomics metabolomics omics proteomics r rstats task-views transcriptomics

Last synced: 13 Apr 2025

https://github.com/nanoporetech/isonclust2

A tool for de novo clustering of long transcriptomic reads

cdna rna rna-seq transcriptomics

Last synced: 13 Apr 2025

https://github.com/soedinglab/transannot

TransAnnot - a fast transcriptome annotation pipeline

annotation assembly bioinformatics bioinformatics-pipeline transcriptomics

Last synced: 27 Apr 2025

https://github.com/lieberinstitute/vistoseg

Image processing pipeline for spatial projects

matlab spatial transcriptomics visium

Last synced: 16 Aug 2025

https://github.com/almeidasilvaf/hybridexpress

An R package for comparative transcriptomic analyses of hybrids and their progenitors

gene-expression hybrid polyploidy rna-seq transcriptomics

Last synced: 20 Oct 2025

https://github.com/transbiozi/biomm

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

biomm dna-methylation elasticnetregression epigenomics gene-expression genomics go-pathway gwas high-dimensional kegg-pathway machine-learning omics phenotype-prediction random-forest svm transcriptomics

Last synced: 29 Oct 2025

https://github.com/krassowski/gsea-api

Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

bioinformatics cuda enrichment gene-set-enrichment gene-sets gsea pandas pathway-analysis python3 transcriptomics

Last synced: 13 Apr 2025

https://github.com/delosh653/echo

An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators.

bioinformatics bioinformatics-tool circadian circadian-rhythm circadian-rhythmicity echo extended-harmonic-oscillators finding-rhythms omics oscillators proteomics transcriptomics

Last synced: 11 Apr 2025

https://github.com/ocbe-uio/discbio

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

biomarker-discovery jupyter-notebook r-package scrna-seq single-cell-analysis transcriptomics

Last synced: 11 Jul 2025

https://github.com/alleninstitute/scrattch.io

Functions for handling RNA-seq files and formats as input and output for scrattch functions.

10xgenomics hdf5 loom r tome transcriptomics

Last synced: 03 Aug 2025

https://github.com/JRaviLab/compbio-gists

Computational Biology & Bioinformatics Resources

bioinformatics comparative-genomics computational-biology data-science gists molecular-evolution phylogeny r shell transcriptomics

Last synced: 07 Oct 2025

https://github.com/wukevin/rnagps

Interpretable model of sub-cellular RNA localization.

interpretable-machine-learning transcriptomics

Last synced: 10 Apr 2025

https://github.com/theislab/mapqc

MapQC - a metric for the evaluation of single-cell query-to-reference mappings

atlas integration mapping query-to-reference-mapping single-cell transcriptomics

Last synced: 11 Oct 2025

https://github.com/alleninstitute/tasic2016data

Single cell transcriptomic data from Tasic, et al. (2016)

scrattch scrna-seq-data transcriptomics

Last synced: 11 Apr 2025

https://github.com/paccmann/paccmann_omics

Generative models for transcriptomics profiles and proteins

deep-learning generative-model proteomics transcriptomics vae variational-autoencoder

Last synced: 10 Apr 2025

https://github.com/UcarLab/iasva

Iteratively Adjusted Surrogate Variable Analysis

heterogeneity heuristic-algorithm r single-cell single-cell-rna-seq transcriptomics

Last synced: 08 Apr 2025

https://github.com/benfulcher/allensdk

Workflow for retrieving spatial gene-expression data from the Allen Institute's Mouse Brain Atlas

bioinformatics geneexpression transcriptomics

Last synced: 13 May 2025

https://github.com/tnaake/matrixqcvis

metabolomics proteomics qc r shiny transcriptomics visualization

Last synced: 10 Apr 2025

https://github.com/noncodo/bigredbutton

Pipeline for the unsupervised clustering of homologous RNA structure motifs from sequencing data.

bioinformatics genome-annotation lncrna rna-structure transcriptomics

Last synced: 21 Jan 2026

https://github.com/dev-ev/prot-rna-umap-clustering

Joint UMAP embedding and clustering of proteomic and transcriptomic data

clustering jupyterlab mass-spectrometry proteomics proteomics-data-integration tmt-data-analysis transcriptomics umap

Last synced: 28 Dec 2025

https://github.com/zavolanlab/zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

bioinformatics cli command-line-interface fair high-throughput library pipeline python reproducible-research rna-seq sequencing snakemake transcriptomics workflow

Last synced: 16 Jan 2026

https://github.com/lieberinstitute/visium_spg_ad

Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.

alzheimers-disease bioconductor rstats spatial-transcriptomics transcriptomics visium visium-spg visium-spg-ad

Last synced: 06 Jan 2026

https://github.com/anergictcell/atg

A Rust library and CLI tool to handle genomic transcripts

bioinformatics bioinformatics-tool cli-app converter genomics gtf transcriptomics

Last synced: 24 Apr 2025

https://github.com/gurbaaz27/cs690a-clustering-spatial-transcriptomics-data

Course Assignment on Clustering of Spatial Transcriptomics Data

cancer-genomics clustering computational-biology computational-genomics deep-learning gene-expression k-means-clustering leiden-algorithm louvain-algorithm rna-seq spatial-transcriptomics transcriptomics variational-autoencoder variational-autoencoders variational-inference visium

Last synced: 05 Jul 2025

https://github.com/htpusa/moomin.jl

From differential gene expression to metabolic changes

constraint-based-modeling differential-expression gene-expression metabolic-models transcriptomics

Last synced: 11 Apr 2025

https://github.com/microbiomedata/metat

Metatranscriptomics workflow

metatranscriptomics transcriptomics workflow

Last synced: 27 Oct 2025

https://github.com/epigen/macrophage-regulation

Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation

atac-seq bioinformatics crispr crop-seq epigenomics immunology perturb-seq perturbations rna-seq scrna-seq systems-biology systems-immunology time-series transcriptomics

Last synced: 03 Aug 2025

https://github.com/sales-lab/spatialde

R wrapper for SpatialDE

python r spatial-data transcriptomics wrapper

Last synced: 05 May 2025

https://github.com/tcp-lab/biotea

bioTEA - A user friendly tool to perform transcript expression analysis

bioinformatics-tool command-line-tool differential-gene-expression docker linux microarray python transcriptomics

Last synced: 30 Aug 2025

https://github.com/antonkulaga/genotations

A small library to work with ensembl and other annotations in python

annotations bioinformatics ensembl genes genomics gtf polars transcriptomics

Last synced: 07 Sep 2025

https://github.com/a-r-j/tb-resources

List of online databases and resources for Mycobacterium Tuberculosis

computational-biology curated drug-discovery genomics genomics-data genomics-data-sets integration list mycobacterium mycobacterium-tuberculosis omics proteomics proteomics-data proteomics-data-integration proteomics-datasets transcriptomics transcriptomics-data transcriptomics-data-integration transcriptomics-datasets tuberculosis

Last synced: 02 Feb 2026

https://github.com/cogdisreslab/biopathnet

bioinformatics bioinformatics-pipeline ilincs r transcriptomics

Last synced: 18 Jan 2026

https://github.com/microsoft/scfm-datamix

Assessing the influence of training data composition on single-cell foundation model performance

foundation-models genomics rna-seq single-cell transcriptomics

Last synced: 22 Mar 2025

https://github.com/niaid/geneioustraining

Introductory notes on using Geneious (Biomatters) at NIAID

alignment assembly-mapping bcbb-training genetic-analysis genomics phylogenetics rna-seq transcriptomics visualization webinar

Last synced: 25 Jul 2025

https://github.com/raw-lab/metaome_stats

Statistical package for metaome denovo assembly results.

fasta genome metagenome metagenome-assembly metaome-stats metatranscriptomics transcriptomics

Last synced: 16 Jan 2026

https://github.com/dhimmel/stargeo

Generating expression signatures for disease using STARGEO

diseases gene-expression hetionet meta-analysis microarray-data rephetio stargeo transcriptomics

Last synced: 23 Mar 2025

https://github.com/dhimmel/bgee

Extracting anatomy-specific gene expression in humans from Bgee

anatomy bgee gene gene-expression hetionet rephetio transcriptomics tsv

Last synced: 09 Oct 2025

https://github.com/nuno-agostinho/phd-thesis

Developing Web Apps for Analyses of Transcriptomes

transcriptomics webapp

Last synced: 08 Nov 2025

https://github.com/stracquadaniolab/cubseq-nf

CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.

codon-bias codon-optimization codon-usage nextflow rnaseq transcriptomics

Last synced: 17 Oct 2025

https://github.com/saezlab/hepatic-microenviroment

Gut microbiota fuels HCC development by shaping the hepatic inflammatory microenvironment

cancer hcc liver microbiome r transcriptomics

Last synced: 22 Jul 2025

https://github.com/thomasgust/elastic-st

A python data science library to build and analyze biological networks from spatial transcriptomics data. Allows inclusion of spatial information into the networks, going a step beyond graphs derived from scRNA-seq techniques.

bioinformatics biological-networks cython data-science linear-models machine-learning python spatial-transcriptomics spatial-transcriptomics-networks transcriptomics

Last synced: 26 Sep 2025

https://github.com/arunbodd/arunbodd.github.io

The website showcases Arun Boddapati's professional portfolio, emphasizing his expertise as a bioinformatics scientist and machine learning expert.

bioinformatics bioinformatics-analysis bioinformatics-pipeline infectious-diseases machinelearning metagenomics nextflow public-health surveillance transcriptomics

Last synced: 23 Jul 2025

https://github.com/tcp-lab/mtp-db

The Membrane Transport Protein Database

phd-project transcriptomics transportome

Last synced: 22 Feb 2025

https://github.com/k8hertweck/cancer_genomics

Example workflow for cancer genomics analysis using TCGA data

cancer genomics tcgabiolinks transcriptomics

Last synced: 03 Mar 2025

https://github.com/lieberinstitute/deconvo_lute-paper

Contains analysis for the lute software paper

bioconductor deconvolution neuroscience r transcriptomics

Last synced: 16 Jul 2025

https://github.com/saezlab/liver-disease-atlas

Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice

bioinformatics liver-disease meta-analysis transcriptomics workflowr

Last synced: 15 Mar 2025

https://github.com/stefanpeidli/scperturb_snakemake_example

Example repository for analyzing many datasets at once from scperturb.org using snakemake

perturbation-methods single-cell transcriptomics

Last synced: 04 Apr 2025

https://github.com/broadinstitute/temporal-rna-seq-deconvolution

Package for temporal deconvolution of bulk RNA-seq samples using SVI

deconvolution pyro rna-seq single-cell-rna-seq svi transcriptomics

Last synced: 20 Feb 2025

https://github.com/gauravcodepro/genomic-alignment-extraction

A scalable large scale genomic fraction aligner and extractor for the large scale alignment of the genomes and the transcriptomes and process them over the cores for the extraction of the aligned regions. The aligned regions can also be mapped to the length plotter and can be machine trained for specific applications

alignment-algorithms alignmentextract alignments genome genome-annotation genome-assembly genomealignment transcriptome-analysis transcriptomealignment transcriptomics

Last synced: 22 Feb 2025

https://github.com/ellfran-7/cluefish

A specialised workflow designed to enhance the biological interpretation of transcriptomic data series 🎣

interpretation r transcriptomics workflow

Last synced: 26 Oct 2025

https://github.com/sing-group/dreimt-backend

A Java backend for the DREIMT application

drug-repositioning immune-system transcriptomics

Last synced: 03 Jul 2025