stemangiola/tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

Language: R - Size: 95.1 MB - Last synced: about 18 hours ago - Pushed: about 18 hours ago - Stars: 159 - Forks: 23

Liuy12/SCdeconR

Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference

Language: HTML - Size: 37.5 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

jackbibby1/SCPA

R package for pathway analysis in scRNA-seq data

Language: R - Size: 41.2 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 53 - Forks: 4

lpantano/DEGreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Language: R - Size: 51.7 MB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 22 - Forks: 16

Katerina10-cloud/CN-aware-DGE

Language: Jupyter Notebook - Size: 11.7 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

saeyslab/multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Language: HTML - Size: 609 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 89 - Forks: 13

nf-core/differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Language: Nextflow - Size: 7.77 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 45 - Forks: 24

PoisonAlien/beadAnalyze

Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).

Language: R - Size: 220 KB - Last synced: 7 days ago - Pushed: almost 8 years ago - Stars: 8 - Forks: 2

UBrau/ProcessDE

Processing RNAseq data for gene expression analysis

Language: R - Size: 30.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

cbib/DIMet

Differential analysis of targeted Isotope-labeled Metabolomics data

Language: Python - Size: 475 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 2

nf-core/slamseq Fork of t-neumann/slamseq

SLAMSeq processing and analysis pipeline

Language: Nextflow - Size: 4.46 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 7

lisiarend/PRONE

R Package for preprocessing, normalizing, and analyzing proteomics data

Language: R - Size: 40.4 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

federicomarini/ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Language: R - Size: 24 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 29 - Forks: 7

danilotat/UTR_add_extend_GTF

Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.

Language: Python - Size: 34.2 KB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 5 - Forks: 2

ajlekcahdp4/differentiator

derevative calculator

Language: C - Size: 61.5 KB - Last synced: 19 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.6 MB - Last synced: 16 days ago - Pushed: 20 days ago - Stars: 17 - Forks: 6

grimmlab/BookChapter-RNA-Seq-Analyses

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

Language: Shell - Size: 12.7 MB - Last synced: 6 days ago - Pushed: almost 3 years ago - Stars: 37 - Forks: 12

snakemake-workflows/rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Language: Python - Size: 5.39 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 63 - Forks: 41

mejian1/ExopherGeneExpressionProfiling

Bioinformatic analysis of gene expression microarray profiles and DGEs on R and R studio

Language: Jupyter Notebook - Size: 1020 KB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 2 - Forks: 0

parashardhapola/scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Language: Python - Size: 32.6 MB - Last synced: 21 days ago - Pushed: 4 months ago - Stars: 89 - Forks: 12

owkin/PyDESeq2

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

Language: Python - Size: 1.29 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 508 - Forks: 55

madsporse/cellex-gsea

R package to calculate cell specific expression of genes, using an input gene set and a CELLEX dataset.

Language: R - Size: 121 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

metavannier/scRNAseq_analysis_workflow

Single-Cell RNA-seq analysis workflow for 10x Genomics data

Language: R - Size: 2.16 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

hasaru-k/GlimmaV2

interactive plots for differential expression analysis

Language: JavaScript - Size: 34.3 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 23 - Forks: 7

mariachiaragrieco/bulk-RNAseq

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

Language: HTML - Size: 5.96 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

jr-leary7/scLANE

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

Language: R - Size: 28.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 7 - Forks: 2

jr-leary7/scLANE-Revision

code and data relating to the scLANE revision

Language: HTML - Size: 108 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

bhklab/survcomp

R package for performance assessment and comparison for survival analysis

Language: C++ - Size: 4.71 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 9 - Forks: 7

DeplanckeLab/ASAP

ASAP : Automated Single-cell Analysis Pipeline

Language: Java - Size: 170 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 23 - Forks: 10

theislab/diffxpy

Differential expression analysis for single-cell RNA-seq data.

Language: Python - Size: 1.71 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 171 - Forks: 23

QBRC/QBRC_BulkRnaSeqDE Fork of yunguan-wang/QBRC_BulkRnaSeqDE

Analysis pipeline for bulk RNA-seq data

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

heiniglab/scPower

Experimental design framework for scRNAseq population studies (eQTL and DE)

Language: R - Size: 190 MB - Last synced: 23 days ago - Pushed: about 1 month ago - Stars: 41 - Forks: 5

BaderLab/scClustViz

Explore and share your scRNAseq clustering results

Language: R - Size: 696 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 44 - Forks: 9

ejmackrell/tidyproteomics-interactive

Interactive Shiny application for tidyproteomics

Language: R - Size: 6.77 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 0

MarioniLab/PlateEffects2016

Code and manuscript files for Aaron's plate effect paper.

Language: PostScript - Size: 1.41 MB - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 8 - Forks: 3

MarioniLab/LOFMethods2016

Code for Lovorka and Aaron's lncRNA loss-of-function project.

Language: R - Size: 114 KB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

nf-core/lncpipe Fork of likelet/LncPipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Language: Nextflow - Size: 9.05 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 30 - Forks: 16

mzytnicki/srnadiff

Language: R - Size: 5.76 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

noamteyssier/adpbulk

pseudobulking on an AnnData object

Language: Python - Size: 19.5 KB - Last synced: 12 days ago - Pushed: 11 months ago - Stars: 19 - Forks: 1

KatrionaGoldmann/volcano3D

An R package to plot interactive three-way differential expression analysis

Language: HTML - Size: 219 MB - Last synced: 14 days ago - Pushed: 9 months ago - Stars: 31 - Forks: 7

himelmallick/Tweedieverse

Differential analysis of multi-omics data based on the Tweedie distribution

Language: R - Size: 233 KB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 25 - Forks: 4

xzhoulab/iDEA-Analysis

Language: R - Size: 12.1 MB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 7 - Forks: 2

sing-group/my-brain-seq

myBrain-Seq: a Compi pipeline for miRNA-Seq data analysis in neuropsychiatry

Language: R - Size: 8.28 MB - Last synced: 1 day ago - Pushed: about 1 year ago - Stars: 6 - Forks: 1

jazminvaleriano/RNAseq-differential-expression

Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.

Language: Shell - Size: 272 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

pblumenkamp/Curare

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Language: Python - Size: 47.3 MB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 7 - Forks: 1

CCBR/MAAPster

MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data

Language: R - Size: 50.5 MB - Last synced: 28 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 6

urmi-21/csvtoxl

Easily convert csv/tsv to excel (xlsx) taking care of gene names or other data vulnerable to auto conversion by MS-Excel

Language: Java - Size: 1.88 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

tarsus-lam/openai-jupyter-integration

Performing scRNA-Seq analysis using OpenAI API calls

Language: Jupyter Notebook - Size: 78.4 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

LeonardoHDL/GP2_Transcriptomics_PDD_PDNCI

This repository contains scripts for differential expression analysis (DEA). From data handling to the DEA. This analysis were made to test DEG from PDD (Parkinson's Disease Dementia)

Language: Jupyter Notebook - Size: 576 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

aidenfmunro/Differentiator

Language: C++ - Size: 1.65 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

annakatsiki/dexplore

DExplore: an online tool for detecting differentially expressed genes from mRNA microarray experiments (www.dexplore.gr, https://hub.docker.com/r/akatsiki/dexplore)

Language: R - Size: 1.03 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 1 - Forks: 1

showteeth/DEbPeak

DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.

Language: HTML - Size: 94.4 MB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 8 - Forks: 1

dmcable/spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Language: HTML - Size: 537 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 225 - Forks: 65

caranathunge/promor

A comprehensive R package for label-free proteomics data analysis and modeling

Language: R - Size: 161 MB - Last synced: 6 months ago - Pushed: 10 months ago - Stars: 10 - Forks: 4

ReaganGen/GEAnaly

An R package for analysis of gene expression matrix with differential expression analysis, enrichment analysis and correlation analysis.

Language: R - Size: 18.7 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

shao-lab/MAnorm

A robust model for quantitative comparison of ChIP-Seq data sets.

Language: Python - Size: 6.87 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 21 - Forks: 5

Pelmeshka127/Differenciator-Machine-Son

Машина Дифференцирования функций, сынок!

Language: C++ - Size: 1.73 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

fcomitani/tapir

Transcriptiome Analysis in Python Imported from R

Language: Python - Size: 9.11 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

btmonier/vidger

Make rapid visualizations of RNA-seq data in R

Language: R - Size: 4.25 MB - Last synced: 19 days ago - Pushed: almost 5 years ago - Stars: 17 - Forks: 6

ncrna/Yeskit

Yet another single-cell analysis toolkit

Language: HTML - Size: 4.54 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 5 - Forks: 0

SiWolf/SCORE

SCORE - a consensus tool for detecting differentially expressed genes in bacteria

Language: R - Size: 1.26 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 5 - Forks: 4

Russel88/DAtest

Compare different differential abundance and expression methods

Language: R - Size: 1.54 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 46 - Forks: 9

fanglab/BEAST

Bacterial Epigenomics Analysis SuiTe

Language: R - Size: 360 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 9 - Forks: 2

Bohdan-Khomtchouk/Microscope

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

Language: R - Size: 4.14 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 23 - Forks: 16

Bohdan-Khomtchouk/shinyDE

Web server for all differential expression (DE) callers

Language: R - Size: 1.51 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

arnikz/EMF_data_mining

Command-line tools in R/Python to analyze semi-quantitative mass spectrometry data on EMF exposures

Language: R - Size: 23.9 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

rbr7/single-cell_rna-seq

Algorithms and functions for working with single cell RNA-seq datasets. (in progress)

Language: R - Size: 4.88 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

tdayris-perso/rna-dge-salmon-deseq2 📦

Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

Language: Python - Size: 3.15 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2

mperalc/Perez-Alcantara-et-al-2018

Scripts used in "Patterns of Differential Gene Expression in a Cellular Model of Human Islet Development, and Relationship to Type 2 Diabetes Predisposition"

Language: R - Size: 57.6 KB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

csbbcompbio/CSBB-v3.0

CSBB - Computational Suite For Bioinformaticians and Biologists

Language: Perl - Size: 4.7 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 6 - Forks: 7

ReemaSingh/Dictostelium_Differential_Expression_Experiment

Identify Differential Expressed Genes in DgcA null mutant and Knock-out samples in Dictyostelium discoideum. The same workflow has been used for the differential expression analysis of Polysphondylium pallidum.

Language: R - Size: 12.7 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

kn-bibs/pathways-analysis

Testing, development environment for a new project of KN BIBS

Language: Python - Size: 147 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 10

Lin-Yux/RankComp

Differential expression genes (DEGs) obtaining methods by R language.

Language: R - Size: 8.06 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

noamteyssier/idea

Integrated Differential Expression and Annotation

Language: HTML - Size: 2.63 MB - Last synced: 19 days ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

KTH-Emil/Venous-thromboembolism-plasma-biomarkers

The following code was used to analyze and vizualise the data in the thesis: "Detecting plasma biomarkers in patients with venous thromboembolism using proximity extension assay"

Language: HTML - Size: 25.1 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

XZouProjects/scCODE

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data

Language: R - Size: 39.2 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 13 - Forks: 6

leahkemp/smncrna_analysis_template

Small non-coding RNA analysis template for analysing Illumina small RNAseq data.

Language: HTML - Size: 187 MB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

leahkemp/rna_analysis_template

Analysis template for analysing Illumina RNAseq data.

Language: HTML - Size: 60.7 MB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

nunofonseca/irap

integrated RNA-seq Analysis Pipeline

Language: R - Size: 2.13 GB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 79 - Forks: 35

theislab/batchglm

Fit generalized linear models in python.

Language: Python - Size: 3.17 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 26 - Forks: 9

aedanr/PhD-Project-2.3

Comparing hierarchical models to existing methods on simulated and recount data

Language: R - Size: 10.8 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

awakenedhaki/moltenpeaks

Package for volcano plot visualization

Language: R - Size: 15.6 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

pentalpha/r-peridot

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

Language: Java - Size: 18.9 MB - Last synced: 10 days ago - Pushed: over 4 years ago - Stars: 4 - Forks: 0

AlexsLemonade/refinebio-examples

Example workflows for refine.bio data

Language: HTML - Size: 773 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 10 - Forks: 5

diyadas/HBC-regen

Code and resources related to the olfactory regeneration project

Language: R - Size: 162 KB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 3

roblehmann/marineHeatwave

Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"

Size: 563 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

jyu-theartofml/RNA_seq_diff_expression

Differential expression analysis in R for RNA sequence reads of fission yeast.

Language: R - Size: 515 KB - Last synced: 10 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

Robaina/Dokdonia

Source code employed in the study: Gene expression response to temperature acclimation in a model photoheterotrophic marine flavobacterium

Language: Python - Size: 238 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

namini94/SimCD

SimCD: Simultaneous Clustering and condition-specific Differential expression analysis for single-cell transcriptome data

Language: R - Size: 3.54 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

niqolla/ieo_RNAseq_project

eproduciton of a publication regarding gene expression in different phases of lactation in humans

Language: TeX - Size: 22.6 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

himelmallick/TweedieLabs

Collection of walkthrough tutorials on how to use Tweedieverse for differential analysis of omics data.

Language: HTML - Size: 57.6 KB - Last synced: 14 days ago - Pushed: about 2 years ago - Stars: 3 - Forks: 0

htpusa/moomin.jl

From differential gene expression to metabolic changes

Language: Julia - Size: 119 KB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

LankyCyril/GLOpenAPI

NASA GeneLab Open API

Language: Python - Size: 5.88 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 1

kandarpRJ/epidecodeR

Online version of tool is live

Language: R - Size: 2.31 MB - Last synced: 6 months ago - Pushed: almost 3 years ago - Stars: 3 - Forks: 0

htpusa/moomin

MOOMIN is a tool for analysing differential expression data

Language: MATLAB - Size: 95.7 KB - Last synced: 11 months ago - Pushed: almost 4 years ago - Stars: 7 - Forks: 0

peterlipan/DE_rpy2

Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2

Language: Jupyter Notebook - Size: 115 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 10 - Forks: 0

NehaSontakk/RNA-sequencing-fastq-to-differential-gene-expression

RNA sequencing processing and analysis to find differential expression

Language: Jupyter Notebook - Size: 6.06 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 1

stemangiola/bioc_2020_tidytranscriptomics

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Language: R - Size: 48.5 MB - Last synced: 4 months ago - Pushed: over 3 years ago - Stars: 26 - Forks: 10

rmoffitt/GeneSetMatch

A tool for deep statistical analyses and informative visualizations of complex -omic data

Language: HTML - Size: 189 MB - Last synced: 12 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

ajandria/futuriandge

This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.

Language: Groovy - Size: 2.86 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0