snaketron/IgGeneUsage

Comparison of gene usage in immune repertoires under different biological conditions

Language: R - Size: 281 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 6 - Forks: 1

pblumenkamp/Curare

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

Language: Python - Size: 47.2 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 8 - Forks: 1

nuno-agostinho/psichomics

Interactive R package to quantify, analyse and visualise alternative splicing

Language: R - Size: 62.9 MB - Last synced at: about 8 hours ago - Pushed at: about 9 hours ago - Stars: 37 - Forks: 11

thom-99/GSE192860

differential gene expression analysis of Data from the study titled: 'Antipsychotic drug trifluoperazine as a potential therapeutic agent against nasopharyngeal carcinoma'

Language: Jupyter Notebook - Size: 3.21 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 1 - Forks: 1

breimanntools/xomics

Python framework for explainable omics analysis

Language: Jupyter Notebook - Size: 16.2 MB - Last synced at: 16 days ago - Pushed at: 9 months ago - Stars: 7 - Forks: 0

nanoporetech/pipeline-transcriptome-de 📦

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Language: Python - Size: 124 KB - Last synced at: 15 days ago - Pushed at: about 2 years ago - Stars: 108 - Forks: 26

myles-lewis/glmmSeq

Gene-level general linear mixed model

Language: R - Size: 13.9 MB - Last synced at: 30 days ago - Pushed at: 3 months ago - Stars: 20 - Forks: 10

jaychowcl/DE_RNAseq_crawler

A differential expression analysis pipeline for bulk RNAseq data with data fetching!

Language: Shell - Size: 557 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

NBISweden/workshop-RNAseq

Workshop • Analysis of RNA-seq data

Language: CSS - Size: 685 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 35 - Forks: 15

genecell/Emergene

Individual cell-based differential transcriptomic analysis across conditions

Language: Python - Size: 13.7 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

mathilde733/RNA-seq

Project on RNA sequencing data

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12danielLL/Neurogenomics_Project

This project focuses on analyzing sequencing data to understand molecular mechanisms of neurological diseases and predict the effectiveness of immunotherapy in breast cancer patients. It integrates Python and R scripts for data processing, statistical analysis, and visualization, alongside a comprehensive report detailing methods and findings.

Language: Jupyter Notebook - Size: 2.7 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Arnaroo/INDEGRA

Accurate, easy and integrated suit to compare RNA samples with different degradation levels, quantify decay rates per-transcript and correct for degradation-induced artifacts in differential gene/transcript comparisons

Language: Python - Size: 158 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

TCP-Lab/bioTEA

bioTEA - A user friendly tool to perform transcript expression analysis

Language: Python - Size: 15.7 MB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 3 - Forks: 2

vertesy/DatabaseLinke.R

A set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

Language: R - Size: 143 KB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

ben-laufer/RNA-seq

RNA-seq alignment and analysis pipeline

Language: R - Size: 35.2 KB - Last synced at: 5 months ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 4

DeplanckeLab/ASAP

ASAP : Automated Single-cell Analysis Pipeline

Language: Java - Size: 170 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 23 - Forks: 10

viktormiok/TempOseq_CarcinoChemMCF-7

Cellular​ ​signatures​ characterisation ​after​ ​carcinogenic​ ​chemical​ ​exposure​ ​in​ ​mammalian​ ​tissue.

Language: HTML - Size: 582 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 3 - Forks: 0

kashiff007/RNA-seq-Pipeline-Under-Construction-

Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.

Language: Shell - Size: 146 KB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

Rajashreeu/Bversity-Capstone-project-

Language: HTML - Size: 801 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

DebmalyaSen34/Lasso-ElasticNet-regression-in-Lung-Cancer

This repository contains a Jupyter Notebook for the analysis of Non-Small Cell Lung Cancer (NSCLC) data using various machine learning techniques.

Language: Jupyter Notebook - Size: 47.2 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

wdecoster/DEA.R

Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

Language: R - Size: 71.3 KB - Last synced at: 13 days ago - Pushed at: over 6 years ago - Stars: 17 - Forks: 7

rohan-b-84/dge_analysis_using_DESeq2

Differential Gene Expression analysis in R using DESeq2

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YogiOnBioinformatics/Teaching-Assistant-Computational-Genomics

Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.

Language: Shell - Size: 809 KB - Last synced at: 12 months ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1

csoderlund/TCW

Analysis of single and comparative transcriptomes

Language: Java - Size: 32.2 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0

cankocagil/BioStatistics

Differential Gene Expression, Phylogenetic tree, Sequence Alignments, Biostatistics, Bioinformatic

Language: R - Size: 3.97 MB - Last synced at: 12 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

viktormiok/tigaR

Temporal Integrative Genomics Analysis in R

Language: R - Size: 926 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

GrosseLab/BGSC

Bayesian Gene Selection Criterion (BGSC) approach

Language: R - Size: 15.6 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

Amandahsr/LSM3241_MicroarrayDifferentialAnalysis

NUS LSM3241: Differential Gene Analysis of Telomere Microarray Data

Language: R - Size: 521 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

iamandreatonina/Laboratory_Biological_Data_Mining

Laboratory of biological Data Mining :computer:

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slowkow/fibrotime

:tangerine: View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

Language: Jupyter Notebook - Size: 267 MB - Last synced at: 8 days ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 0

meeranhussain/RNASeq_DEGseq_Snakemake_NO-REPLICATES

Workflow for differential gene expression analysis for non-replicate samples using DEGseq

Language: R - Size: 20.5 KB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

meeranhussain/RNASeq_Deseq2_Snakemake

Differential gene expression analysis for samples with replicates using STAR-DeSeq2 pipeline

Language: R - Size: 46.9 KB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

PiotrTymoszuk/collagen_pca

Expression, biological and clinical relevance of the collagen pathway genes in prostate carcinoma

Language: R - Size: 144 MB - Last synced at: 8 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

labsyspharm/dubportal

An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportal

Language: HTML - Size: 346 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

PaulaRS/Comparative_DGE_Enrichment

R scripts and input data for RNAseq differential gene expression without a reference genome.

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YogiOnBioinformatics/Differential-Gene-Expression-Analysis-with-Machine-Learning-Using-Dexamethasone-Treatment-Data

Worked with fellow peers at University of Pittsburgh under supervision of Dr. Junshu Bao, Department of Statistics, University of Pittsburgh, to do a Differential Gene Expression Analysis on a Dexamethasone treatment data set and incorporated Machine Learning into project.

Language: R - Size: 400 KB - Last synced at: 12 months ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 2

kmyafi/Breast-Cancer-Differential-Gene-Expression-Analysis

Differential Gene Expression (DGE) Analysis in Curated Microarray Data of Breast Cancer Subtypes

Language: R - Size: 924 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

DISC-IISR/RNAseqAnalysis

The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction

Language: R - Size: 126 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

bixBeta/DESeq2Shiny2

DESeq2Shiny2 is an R shiny application to handle NGS count data and perform unsupervised clustering and Differential Gene Expression Analysis using DESeq2.

Language: R - Size: 112 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

BenaroyaResearch/SPresnell_GSE147507

GSE147507 SARS-Cov-2 Dataset from Mt. Sinai

Size: 15.1 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 2

GrosseLab/VipeR_HIF1alpha

Viper is a Snakemake workflow, aimed at performing the RNA-seq workflow of the paper 'Causes and consequences of a glutamine induced normoxic HIF1 activity for the tumor metabolism', Kappler et al. (2019) in a reproducible and automated manner

Language: R - Size: 13.1 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 5 - Forks: 0

AngryMaciek/snakemake_qdgedtu 📦

RNA-Seq data analysis: Quantification, Differential Gene Expression, Differential Transcripts Usage

Language: R - Size: 83 KB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

pblumenkamp/GenExVis

An application for exploring and visualizing differential gene expression data created with DESeq2

Language: Vue - Size: 32.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

xzhoulab/iDEA

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

Language: C++ - Size: 21.2 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 26 - Forks: 9

bio2bel/adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

Language: Python - Size: 21.5 KB - Last synced at: 11 days ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

kpatel427/DE_analysis

Scripts to run differential expression analysis using DESeq2 package

Language: R - Size: 8.79 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 2

cemalley/scRNASeq-bulkRNASeq

single cell and bulk RNASeq analysis scripts

Language: HTML - Size: 327 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 9

koushik20/BRCA_RNA-Seq_Analysis

RNA-seq analysis workflow using DESeq2

Language: R - Size: 1.94 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

csquires/dci

Code and figures for the Differential Causal Inference (DCI) algorithm

Language: Jupyter Notebook - Size: 293 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 0

arkanivasarkar/RNAseq-Data-Analysis-Pipeline

Pipeline for analyzing RNAseq data of human and mouse - beginner friendly with minimal user inputs

Language: R - Size: 1.52 MB - Last synced at: 25 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

sbg/GENAVi Fork of alpreyes/GENAVi

Example R Shiny app demonstrating Seven Bridges Platform integration via OAuth2.

Language: HTML - Size: 162 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

bissessk/Whole-Genome-Bioinformatic-Analysis-of-Skin-from-Three-Immunologically-Diverse-Mouse-Models

Performed a differential gene expression analysis with RNA-seq on three immunologically diverse mouse models. Differentially expressed genes were identified and a GO term enrichment analysis was done to determine their roles.

Size: 2.89 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

jonbra/NGS-Abel

Bioinformatic scripts for working on the UiO Abel compute cluster

Language: Shell - Size: 41 KB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

bixBeta/betaBox

DEMUX, ALIGN, DESEQ2 DGE CALLS

Language: Shell - Size: 1.01 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0