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bulk-rna-seq

Here are 29 public repositories matching this topic...

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

Updated Dec 3, 2022
R

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

Updated Feb 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

Updated Jun 20, 2022
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

Updated Dec 24, 2022
Java

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

Updated Jan 21, 2023
Python

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

Updated Jan 19, 2023
R

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

Updated Apr 19, 2020
R

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

Updated Oct 25, 2022
Python

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

Updated Jan 13, 2022
HTML

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

Updated Jan 23, 2023
Python

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

Updated Oct 22, 2022
Python

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

Updated Mar 4, 2021
Jupyter Notebook

QBRC / QBRC_BulkRnaSeqDE

Analysis pipeline for bulk RNA-seq data

alignment differential-expression bulk-rna-seq

Updated Aug 18, 2022
Python

Zhuang-Bio / miRNAprofiling

miRNA and mRNA profiling of human wounds

bulk-rna-seq wound-healing

Updated Jan 24, 2023
HTML

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

Updated Jan 7, 2023
R

Functional-Genomics / CATD

CATD: Critical Assessment of Transcriptomics Deconvolution

benchmarking scrna-seq deconvolution bulk-rna-seq

Updated Sep 16, 2021
R

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

Updated May 27, 2022
Shell

Amirreza-Mousavi / Rodriguez2017_RNA_Seq_Analysis_Replication

In this repository, I try to replicate the results of Rodriguez2017

shell rna-seq r rna-seq-pipeline bulk-rna-seq

Updated Jun 18, 2022
Shell

crhisto / MuSiC

Multi-subject Single Cell Deconvolution

deconvolution non-negative-matrix-factorization bulk-rna-seq

Updated Feb 12, 2021
R

poloarol / scrna-analysis-tutorials

scRNA Analysis tutorials

python bioinformatics r tutorials bioinformatics-pipeline transcriptomics bioinformatics-analysis single-cell-rna-seq seurat bulk-rna-seq scanpy scvi-tools

Updated Jan 23, 2023
HTML

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