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.

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Starlitnightly/omicverse

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

Language: Jupyter Notebook - Size: 1.34 GB - Last synced at: 4 days ago - Pushed at: 7 days ago - Stars: 614 - Forks: 76

bcgsc/RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads

Language: Java - Size: 2.41 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 103 - Forks: 8

LieberInstitute/Habenula_Pilot

habenulaPilot project code repository

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allyssonallan/schizoplacenta

Code to handle RNA-seq analysis with placenta bulk data

Language: R - Size: 141 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

WolfrumLab/MHUO

Unveiling adipose populations linked to metabolic health in obesity

Language: R - Size: 1.02 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 2

earmingol/cell2cell

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

Language: Python - Size: 99.7 MB - Last synced at: 8 days ago - Pushed at: 11 months ago - Stars: 60 - Forks: 17

neurogeek03/Thesis_Alternative_Polyadenylation

A study of Alternative Polyadenylation in developing cortical neurons (timepoints: 0, 4, 30 days) in bulk RNA-seq data. Several lengthening events over time were identified.

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carpentries-incubator/bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

Language: R - Size: 53.1 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 22 - Forks: 36

stef1949/RNA-Seq-Preprocessing-Scripts

This repository contains a collection of preprocessing scripts designed to help streamline data preparation tasks.

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dalmolingroup/bulkrna

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

Language: Groovy - Size: 4.89 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 8 - Forks: 1

auroramaurizio/my_RNA_seq_pipelines

my_RNA_seq_pipelines

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namini94/EXPORT

EXPORT: Explainable VAE for ordinally perturbed transcriptomics data

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luuloi/AppliedBioinformatics2023

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

Language: R - Size: 274 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 9 - Forks: 5

utdal/Bulk-RNA-Seq-Nextflow-Pipeline

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

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DerekBreton1/Bulk-RNAseq-Analysis

End-to-end pipeline for analyzing bulk RNA-sequencing data

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nunofonseca/irap

integrated RNA-seq Analysis Pipeline

Language: R - Size: 2.13 GB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 83 - Forks: 34

carpentries-incubator/workflows-nextflow

Workflow management with Nextflow and nf-core

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futianfan/GenoCraft

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

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hms-dbmi/dseqr

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

Language: R - Size: 36.9 MB - Last synced at: 30 days ago - Pushed at: 7 months ago - Stars: 20 - Forks: 4

Zhuang-Bio/miRNA_mRNA_profiling_paper_scripts

bulk RNA-seq of miRNA and mRNA profiling of human acute and chronic wounds

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U-BDS/bulk_RNA_seq_workshop

Workshop materials for the U-BDS bulk RNA-seq lessons

Language: R - Size: 53.4 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 2

euxhenh/Truffle

Trajectory Inference of clinical data via Multi-commodity Flow

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nasqar/deseq2shiny

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

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digitalcytometry/ecotyper

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

Language: R - Size: 663 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 151 - Forks: 38

mariachiaragrieco/bulk-RNAseq

bulk-RNAseq analysis for Transcriptomics Course 2021 (MSc Bioinformatics for Computational Genomics)

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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

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QBRC/QBRC_BulkRnaSeqDE Fork of yunguan-wang/QBRC_BulkRnaSeqDE

Analysis pipeline for bulk RNA-seq data

Language: Python - Size: 216 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

jalwillcox/Calculate-PSI

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

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crhisto/SCDC

SCDC project, originally on: https://github.com/meichendong/SCDC. Support sparse matrix among other additions.

Language: R - Size: 134 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

crhisto/thymus_NPM-ALK_notebook

R Notebook with scripts for running the deconvolution of thymus bulk data identifying T-cell proportions

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crhisto/CRC_organoids_and_fibroblasts_notebook

Deconvolution of CRC in organoid and fibroblast bulk data identifying epithelial cell types proportions

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crhisto/DecoFlex

DecoFlex deconvolution method for Omic data implemented as DecoFlexR

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ebi-gene-expression-group/selectBCM

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

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maxozo/eqtl Fork of wtsi-hgi/eqtl

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ecianini/bulk_RNA-Seq

Project for the Transcriptomic course of "Bioinformatics for Computational Genomics" MSc

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weng-lab/rnaseq-workflow

RNA-seq pipeline, based on the ENCODE uniform processing pipeline

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Functional-Genomics/CATD

CATD: Critical Assessment of Transcriptomics Deconvolution

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Danko-Lab/TED

a fully Bayesian approach to deconvolve tumor microenvironment

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poloarol/scrna-analysis-tutorials

scRNA Analysis tutorials

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cemalley/scRNASeq-bulkRNASeq

single cell and bulk RNASeq analysis scripts

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metavannier/metatranscriptomics-bulkrnaseq_workflow

This workflow performs a metatranscriptomics and bulk RNAseq analysis from the sequencing output data to the differential expression analyses.

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fanzhanglab/bulk_RNAseq_pipeline

Bulk RNA-seq analytical pipeline, including using Snakemake to run main steps such as Kallisto read mapping, QC, Principal Component Analysis (PCA), and other downstream analysis.

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Amirreza-Mousavi/Rodriguez2017_RNA_Seq_Analysis_Replication

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

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crhisto/MuSiC Fork of xuranw/MuSiC

Multi-subject Single Cell Deconvolution

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centuri-engineering/differential-expression_workflow

This workflow performs an RNA-seq analysis from the sequencing output data to the differential expression analyses.

Language: R - Size: 10.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1