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bulk-rna-seq

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Starlitnightly /omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

bioinformatics omics single-cell bulk-rna-seq

UpdatedMar 16, 2025
Jupyter Notebook

digitalcytometry /ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

tumor single-cell deconvolution bulk-rna-seq microenvironment

UpdatedMar 28, 2024
R

bcgsc /RNA-Bloom

🌺 reference-free transcriptome assembly for short and long reads

rna-seq denovo-assembly single-cell-rna-seq bioinformatics-tool nanopore-sequencing bulk-rna-seq pacbio-sequencing

UpdatedJan 28, 2024
Java

nunofonseca /irap

integrated RNA-seq Analysis Pipeline

rna-seq pipeline gene-expression rna-seq-analysis differential-expression transcript-quantification single-cell-rna-seq irap bulk-rna-seq exon-quantification

UpdatedFeb 6, 2019
R

Danko-Lab /TED

a fully Bayesian approach to deconvolve tumor microenvironment

scrna-seq deconvolution bulk-rna-seq tumor-cells stromal-cells expression-profile tumor-expression

UpdatedJun 20, 2022
R

earmingol /cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

machine-learning bioinformatics rna-seq computational-biology rnaseq single-cell single-cell-rna-seq bulk-rna-seq sc-rna-seq cell-cell-interaction cell-cell-communication

UpdatedJun 14, 2024
Python

carpentries-incubator /workflows-nextflow

Workflow management with Nextflow and nf-core

nextflow english lesson rna-seq-analysis workflow-management pre-alpha nf-core bulk-rna-seq carpentries-incubator

UpdatedJan 21, 2025
Nextflow

carpentries-incubator /bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

r english bioconductor lesson rna-seq-analysis hacktoberfest pre-alpha life-sciences bulk-rna-seq carpentries-incubator

UpdatedFeb 4, 2025
R

hms-dbmi /dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

rna-seq drug-repurposing single-cell-rna-seq bulk-rna-seq

UpdatedOct 21, 2024
R

futianfan /GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

visualization flask rna-seq genomics ngs next-generation-sequencing protein omics single-cell pathway-analysis omics-data-integration bulk-rna-seq multiomics

UpdatedOct 29, 2024
SCSS

nasqar /deseq2shiny

a web-based R shiny application that wraps DESeq2 R package

visualization bioinformatics rna-seq r shiny rshiny deseq2 rna-seq-analysis shinyapps webapplication bulk-rna-seq

UpdatedApr 19, 2020
R

IGS /gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

rna-seq gene-expression single-cell single-cell-analysis bulk-rna-seq data-archive

UpdatedMar 18, 2025
Jupyter Notebook

cemalley /scRNASeq-bulkRNASeq

single cell and bulk RNASeq analysis scripts

r genomics heatmap deseq2 scrna-seq tsne monocle differential-gene-expression seurat bulk-rna-seq monocle2 fateid tscan

UpdatedJan 13, 2022
HTML

luuloi /AppliedBioinformatics2023

"Applied bioinformatics" is a course for Genetics Master Program at Genetics Department

bioinformatics dna-seq bulk-rna-seq

UpdatedDec 8, 2024
R

dalmolingroup /bulkrna

Dalmolin Group's workflow for pre-processing, alignment and quantification of bulk RNA-seq data

bioinformatics pipeline nextflow expression bulk-rna-seq

UpdatedSep 30, 2024
Groovy

NUPulmonary /2020_Grant

Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper

biology sequencing flow-cytometry single-cell-rna-seq bulk-rna-seq covid-19

UpdatedJul 18, 2023
Jupyter Notebook

euxhenh /Truffle

Trajectory Inference of clinical data via Multi-commodity Flow

time-series crohns-disease psoriasis clinical-data multi-commodity-flow bulk-rna-seq trajectory-inference covid-19 pseudotime-ordering

UpdatedJul 4, 2024
Jupyter Notebook

QBRC /QBRC_BulkRnaSeqDE

Analysis pipeline for bulk RNA-seq data

alignment differential-expression bulk-rna-seq

UpdatedAug 18, 2022
Python

jalwillcox /Calculate-PSI

A script used to calculate percent spliced-in (PSI) values from bulk RNA sequencing data.

rna-seq rnaseq psi rna-seq-analysis bulk-rna-seq splicing rna-splicing percent-spliced-in rna-splicing-analysis

UpdatedMay 27, 2022
Shell

ebi-gene-expression-group /selectBCM

An R tool to detect and correct batch-effects in gene-expression data (Microarray and bulk-RNAseq))

gene-expression batch-correction bulk-rna-seq microarray-data-analysis

UpdatedJan 7, 2023
R

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