rna-seq-pipeline | Topic | Ecosyste.ms: Repos

Topic: "rna-seq-pipeline"

GuyTeichman/RNAlysis

Analyze your RNA sequencing data without writing a single line of code

Language: Python - Size: 797 MB - Last synced at: 11 days ago - Pushed at: about 2 months ago - Stars: 135 - Forks: 13

urmi-21/pyrpipe

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Language: Python - Size: 204 MB - Last synced at: 16 days ago - Pushed at: about 4 years ago - Stars: 84 - Forks: 28

gaolabtools/scNanoGPS

Single cell Nanopore sequencing data for Genotype and Phenotype

Language: Python - Size: 27 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 51 - Forks: 5

uc-bd2k/GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator

Language: HTML - Size: 38.2 MB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 49 - Forks: 19

jumphone/SPRINT

SNP-free RNA editing Identification Toolkit

Language: Python - Size: 10.8 MB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 47 - Forks: 19

Taiji-pipeline/Taiji

All-in-one analysis pipeline

Language: Haskell - Size: 4.05 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 31 - Forks: 8

NCBI-Hackathons/SPeW

Automatic Packaging and Distribution of Bioinformatics Pipelines

Language: Python - Size: 904 KB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 26 - Forks: 8

giuliospinozzi/arpir

Automatic RNA-Seq Pipelines with Interactive Report

Language: R - Size: 202 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 25 - Forks: 11

PalMuc/TransPi

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Language: Nextflow - Size: 48.6 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 24 - Forks: 14

HKU-BAL/Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Language: Python - Size: 528 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 22 - Forks: 1

uc-bd2k/GREP2

GEO RNA-seq Experiments Processing Pipeline

Language: R - Size: 2.11 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 20 - Forks: 10

egaffo/CirComPara

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

Language: R - Size: 16 MB - Last synced at: 19 days ago - Pushed at: about 5 years ago - Stars: 16 - Forks: 11

eonurk/RNA-seq-differential-analyses-guideline

A quick recap of widely used differential analyses methods in R for RNA-seq experiments

Size: 336 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 14 - Forks: 3

BleekerLab/snakemake_rnaseq

A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)

Language: Python - Size: 85.4 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 8

epigen/rnaseq_pipeline

RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

Language: Python - Size: 104 KB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 10 - Forks: 2

schosio/CHOLAR

Automated RNA-seq pipeline for lncRNA indentification

Language: Shell - Size: 33.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 1

cellgeni/rnaseq

Fast RNAseq pipeline

Language: Groovy - Size: 7.95 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 4

zqfang/snakeflow

bioinfo workflow based on snakemake

Language: Python - Size: 7.94 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 7

vondoRishi/4-RNA-seq

A slurm based pipeline for RNA-seq analysis to execute on linux clusters. Feel free to connect to visualize your RNA-seq data on the clouds

Language: HTML - Size: 3.62 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 3

zavolanlab/PAQR2

Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.

Language: Python - Size: 36.5 MB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

hanielcedraz/BAQCOM

Quality Control, Mapping and Reads Count for RNA-Seq Analysis

Language: R - Size: 102 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 1

czheluo/Teach-Bioinformatics-R-dataviz

Materials for "Teaching Bioinformatics and R for dataviz course" June-August 2019 in Majorbio

Language: R - Size: 28 MB - Last synced at: 3 months ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 4

LieberInstitute/SPEAQeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

Language: HTML - Size: 770 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 4

DKFZ-ODCF/RNAseqWorkflow

Roddy RNA-seq Workflow Plugin

Language: Perl - Size: 832 KB - Last synced at: 6 months ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 4

RuzhangZhao/mixhvg

The package mixhvg uses mixture of highly variable gene selection methods to improve gene selection.

Language: R - Size: 5.37 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 1

mhjiang97/RNASeqFlow

A small python tool for RNA-seq workflows

Language: Python - Size: 302 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0

EmoryIntegratedComputationalCore/Methods

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

Language: R - Size: 18 MB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

LappalainenLab/RNApipeline

Language: Shell - Size: 43.9 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 1

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: over 1 year ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 0

galantelab/fredy

Tool to identify chimeric events from RNA-Seq data

Language: Shell - Size: 23.4 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 4 - Forks: 0

apredeus/multi-bacpipe

A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments

Language: Perl - Size: 2.15 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 2

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 at: 3 months ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 0

niekwit/rna-seq-star-tetranscripts

Snakemake workflow for transposable element RNA-Seq using TEtranscripts

Language: R - Size: 95.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

vivekruhela/miRPipe

miRPipe: Open source RNA-Seq bioinformatics analysis docker for identification of miRNAs and piRNAs

Language: Python - Size: 99.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 3

Lexogen-Tools/quantseqpool_analysis

Standard analysis routine for samples that were generated with Lexogen's QuantSeq pool library preparation kit.

Language: Shell - Size: 6.37 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 2

furkanmtorun/rna-seq-workflow 📦

🛠 under active development | RNA-Seq Workflow in Jupyter Notebook

Language: Jupyter Notebook - Size: 30.3 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

pentalpha/r-peridot-gui

The power of the R's differential gene expression analysis packages, with no programming required.

Language: Java - Size: 62.2 MB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

sing-group/dewe

DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.

Language: Java - Size: 1.38 MB - Last synced at: 27 days ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0

scienceforever/GLSeq

Pipeline for low-level RNA-Seq data processing

Language: R - Size: 718 KB - Last synced at: 4 months ago - Pushed at: almost 9 years ago - Stars: 3 - Forks: 0

Norreanea/SmedAnno

SmedAnno is a robust RNA-Seq annotation pipeline designed to streamline analysis from raw reads to a comprehensive, functionally annotated gene set. It handles short reads, long reads, or a combination of both, and provides extensive quality control metrics to help identify potentially fragmented or chimeric gene models.

Language: Shell - Size: 14.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0

navduhan/pyseqrna

pySeqRNA: a python-based package for RNASeq data analysis

Language: Python - Size: 1.18 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 3

jlchen5/RNA-seq-Analysis

This repository contains RNA-seq analysis scripts.

Language: R - Size: 13.7 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - 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: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

rnabioco/rhumba

Snakemake pipelines for RNA sequencing data

Language: C - Size: 21.2 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 2

francescopatane96/RNA-seq_Pipeline

Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...

Language: Jupyter Notebook - Size: 31.3 KB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

CasillasAlba/GeneFlow

GeneFlow is a scalable and flexible software library that encompasses data acquisition methods, preprocessing techniques, data analytics, data visualization, and Machine Learning algorithms that can be applied to genomic data.

Language: Jupyter Notebook - Size: 8.94 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

naoto-hikawa/RNAseq_tutorial

Tutorial for RNA sequence data processing and simple downstream analysis with Drosophila melanogaster

Language: Python - Size: 83.7 MB - Last synced at: 8 months ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

evolomics-group/rna-seq-pipeline

In development scripts for EvolOMICs group's NGS Data Analysis Pipeline

Language: Shell - Size: 3.48 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

egaffo/circompara-docker

:whale: Docker image for CirComPara

Language: Dockerfile - Size: 6.84 KB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

tluquez/QUARS

QUAlity control for RNA_Seq, a nextflow pipeline

Language: Groovy - Size: 2.58 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 2

BimberLab/nimble

nimble — execute lightweight, flexible alignments on custom reference libraries

Language: Python - Size: 215 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

Lioscro/alaska-parse

Automated and friendly RNA-seq analysis (migrated to Parse Server)

Language: JavaScript - Size: 4.02 MB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

jawa23bio/RNA-Seq

RNA-Seq analysis pipeline for investigating transcriptional changes during mammalian cardiac regeneration.

Language: HTML - Size: 985 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

angai4/FYP

RNA-seq pipeline automation scripts

Language: Perl - Size: 674 KB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

deeprob/rnaseq_analysis

Girirajan Lab RNA-seq analysis pipeline

Language: Python - Size: 206 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 4

Marval96/RNAseq_uivc

This repository is for differential expression analysis of RNAseq bulk data.

Language: Jupyter Notebook - Size: 8.31 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

gih0004/RNA_seq_pipeline

RNA seq pipeline designed for paired end reads using HTSEQ for producing files needed for visualizing transcriptomic data with DESEQ2

Language: Shell - Size: 36.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

10adavis/DESeq2_fGSEA_Flow

This repo is a template for running differential gene expression analysis of RNA-seq count data followed by gene set enrichment analysis. This workflow is run in R using Rmarkdown. It is based around the popular R packages, DESeq2, fGSEA, and others.

Language: R - Size: 7.22 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

sivkri/miRNASeq-DE-Analysis-QC

Performing RNA-Seq data analysis and quality control using DESeq2 in R.

Language: R - Size: 110 KB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

milescsmith/rnaseq_targets_pipeline

An R {targets}-based pipeline for processing and generating reports for RNAseq data

Language: R - Size: 97.1 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Sherman-1/Hackathon

RNAseq analysis pipeline project for Paris-Saclay's University Master AMI2B

Language: Nextflow - Size: 84.7 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 2

williamjeong2/snakemake_RNA-seq

A repository for RNA-seq workflow

Language: R - Size: 12.9 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

tjbencomo/rna-pipeline

RNA sequencing pipeline for Stanford's Sherlock HPC cluster

Language: C++ - Size: 90.9 MB - Last synced at: 9 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 2

bissessk/RNA-seq-Analysis-of-Control-and-NRDE2-depleted-Breast-Cancer-Cells

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

Language: Shell - Size: 418 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

MillerLab-CPHG/RNA_Seq-Flow

RNA-Seq Analysis pipeline using Snakemake workflow

Language: Python - Size: 330 KB - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 2

biomystery/RNA-seq-snakemake-pipeline

A snakemake RNAseq pipeline using kalisto. Adapted from https://github.com/crazyhottommy/RNA-seq-analysis/tree/master/RNA-seq-snakemake-pipeline

Language: Python - Size: 1.97 MB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

ydavidchen/RNA-seq Fork of wt2015-github/RNA-seq

Moditifed example of RNA-seq gene expression analysis from scratch

Language: Shell - Size: 33.2 KB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

Osama1452/RNA-Seq-experiment

A state-of-the-art R pipeline for RNA-seq data analysis, optimized for differential expression and functional annotation in mouse models. Features edgeR-based modeling, limma contrasts, and clusterProfiler for GO/KEGG insights. A valuable resource for genomic research and publication.

Language: HTML - Size: 94.8 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

unikill066/Bulk-RNA-Seq-Nextflow-Pipeline Fork of 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.

Language: Nextflow - Size: 4.73 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0

vgkavin/RNAseq

Paired-end bulk RNAseq data preprocessing for counts

Language: Python - Size: 5.93 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

ltor-nyulmc/Masters_Thesis_Multiomic_MG_Macrophage

Analysis code, scripts, and data visualization from my Master's thesis focused on the multiomic integration (transcriptomics, lipidomics, spatial lipidomics) of monoglyceride responses in adipose tissue macrophages within the context of obesity.

Size: 48.8 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

Nwinters29/Bioinformatics

Compilation of scripts pertaining to the field of Bioinformatics

Language: Python - Size: 3.17 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

hingelman/BifrostOmics

A bridge between omics datasets, bioinformatics & non-CS users

Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

jeongahblairlee/rnaseqExplorer

Interactive tools for comprehensive RNA-seq analysis, from data analysis to in-depth visualizations

Language: R - Size: 8.28 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

IdoBar/Mnova_transcriptome_pipeline

Bioinformatics analyses pipelines for transcriptome assembly and annotation of Humpback whale adipose tissue

Language: HTML - Size: 2.29 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

merlinis12/RNA-Seq-Data-Analysis-in-R

RNA-Seq Data Analysis in R: From Raw Counts to Differential Expression Analysis

Language: HTML - Size: 4.05 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

imrobintomar/rna-seq-annotator

A robust Python tool for annotating RNA sequencing data using standardized ontologies and classification systems.

Language: Python - Size: 13.7 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

kristinassong/RNAseq

A Snakemake pipeline to analyze RNA-seq expression data

Language: Python - Size: 117 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

pfrsch/EBAC-workshop

Ciência de Dados na Saúde: Construir um modelo para predizer quando uma pessoa tem câncer dado um exame de sequenciamento do RNA

Language: Jupyter Notebook - Size: 0 Bytes - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

d3b-center/d3b-dev-rnaseq-snv

RNAseq SNV Calling Workflow (beta). This workflow follows the COV-IRT NASA-developed pipeline, with the exception of joint genotyping-specific params and steps.

Language: Jupyter Notebook - Size: 205 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 2

groverkaushal/RNAseq-Workflow-Mapping-Assembly-and-Differential-Gene-Expression-Analysis

This project uses an workflow pipeline to generate map and assemble RNAseq reads to a reference genome. Furthermore, we generate counts data and identify differentially expressed genes from 2 conditions.

Language: Shell - Size: 122 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

dgrfs/NFCore_RNASeq_Cardiff_University_Hawk

RNA Sequencing pipeline on Cardiff University Hawk using NF-Core with example data.

Language: Shell - Size: 22.1 MB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

yjx1217/EvoSeq_RNA

An in-house bioinformatic framework for bulk RNA-seq analysis

Language: HTML - Size: 14.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

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: 5 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ssl-bio/Degradome-analysis

Pipeline for the analysis of degradome sequencing data using the third party PyDegradome (https://github.com/mgaglia81/PyDegradome) script followed by a custom classification. The pipeline requires a custom R package (https://github.com/ssl-bio/R_postpydeg)

Language: Python - Size: 4.46 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0