rnaseq-pipeline

There are 2 repositories under rnaseq-pipeline topic.

Novartis / pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics
Language:Python 28
amarinderthind / RNA-seq-tutorial-for-gene-differential-expression-analysis
This tutorial is created for educational purpose
rnaseq-pipeline rnaseq rnaseq-workshop deseq2 edger enrichment-analysis bioconductor-packages reactome-pathway pca-analysis rna-seq-dge tutorial gene-expression analysis rna-seq r ngs ngs-analysis
Language:R 27
sunyumail93 / PipeRNAseq
A comprehensive pipeline for RNAseq data analysis
rnaseq-pipeline transcriptome-analysis bioinformatics rnaseq bioinformatics-analysis bioinformatics-pipeline gene-expression rna rna-seq-analysis rna-sequencing
Language:Shell 20
eandresleon / miARma-seq
miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis
rnaseq-pipeline rna-seq-analysis mirna mirna-seq circrna-pipeline
Language:Perl 13
ajitjohnson / arseq
An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)
rna-seq-analysis rnaseq-pipeline rna-seq rnaseq
Language:R 9
umccr / RNAsum
Pipeline for generating RNAseq-based cancer patient reports
rnaseq-report rnaseq-pipeline
Language:R 7
CGAT-Group / DICAST
Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.
docker rnaseq-analysis rnaseq-pipeline snakemake transcriptomics
Language:Python 6
czheluo / lncRNA-pipeline
lncRNA analysis pipeline
lncrna-pipeline rnaseq-pipeline
Language:Perl 4
LieberInstitute / SPEAQeasyWorkshop2020
EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.
rstats speaqeasy bioconductor limma rnaseq-pipeline nextflow nextflow-pipelines
Language:R 3
mppl1 / RNAseq_preprocessing
These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline
rnaseq-pipeline hisat2 stringtie transcriptome-assembly differential-gene-expression
Language:Shell 3
kicheolkim / RNAseq_FullTx
RNA-Seq data analysis: whole transcriptome, stranded, dUTP method
rnaseq rnaseq-pipeline rna-sequencing rna-seq rna-seq-analysis
Language:R 2
jvandinter / container_pilot
pilot pipeline that includes tool containerization
ribosome-profiling rnaseq-pipeline
Language:Shell 1
LBGC-CFB / LoRID
Long Read Isoform Discovery tool
longread rnaseq-pipeline
Language:Python 1
milescsmith / rnaseq_pipeline
Snakemake+singularity RNAseq processing pipeline
rnaseq rna-seq rnaseq-pipeline pipeline snakemake bioinformatics-pipeline bioinformatics nextflow
Language:Python 1
nbay13 / toilkit
A python package for working with inputs to and outputs from the toil-rnaseq pipeline
rnaseq-pipeline transcriptomics bioinformatics rnaseq rsem fastqc sequence-alignment
Language:Python 1
PavlidisLab / rnaseq-variant-pipeline
Pipeline for calling and analyzing variants from RNA-Seq data
gatk4 picard star rnaseq-pipeline variant-calling luigi-workflows rnaseq
Language:Python 1
sevdarafatov / RNASeq_snakemake
These snakefiles are prepared for the snakemake pipeline for the RNASeq analysis
python rnaseq-pipeline snakemake
Language:Python 1
tdayris-perso / rna-count-salmon
Snakemake workflow for Salmon quantification and FastQC quality controls
snakemake-workflows bioinformatics-pipeline reproducible-workflows rnaseq-pipeline fastqc salmon multiqc
Language:Python 1
WestGermanGenomeCenter / circrna_detection
circs_snake : a snakemake-based circRNA detection workflow
circular rna rna-seq rna-seq-pipeline rnaseq-pipeline
Language:Python 1
Alruta / Kallisto-DESeq2_Pipeline
A script to analyze with DESeq2 data from Kallisto. You maybe are interested only in DESeq2 part and its analisis and representation :)
deseq2 deseq2-analysis kallisto r rstudio rna-seq rnaseq-analysis rnaseq-pipeline
0
CreedxAsif / Flowchart
This Repository contains various Flowcharts, Visual and Graphical representations which are all created for educational purposes
education elisa diagrams elisa-results flowchart rnaseq-pipeline
0
kiranfranklin999 / Nextflow_tutorials
Introduction to Bioinformatics workflows with Nextflow
nextflow rnaseq rnaseq-pipeline
Language:Nextflow 0
michalbukowski / rnaseq-pipeline-1
Simple Snakemake RNA-Seq pipeline
rna-seq rnaseq-analysis rnaseq-pipeline dge dge-analysis python3 r snakemake snakemake-pipeline snakemake-rna-seq salmon salmon-deseq2 pandas bioconductor miniconda python miniconda3
Language:Python 0
MJBioInfo / SnakemakeWorkflow
In this repository : i have created RNAseq pipeline using snakemake rules
rnaseq-pipeline snakemake-workflow
Language:Python 0
simon-bt / sm-rnaseq-splicing
Snakemake pipeline for alternative slicing analysis with VAST-TOOLS
alternative-splicing rnaseq-analysis rnaseq-pipeline snakemake-workflow vast-tools
Language:Python 0
sup1496 / RNASeq-Analysis
A basic pipeline for the analysis of RNASeq data. Entirely done in Bash and R script.
rnaseq-pipeline bash-script r
Language:Shell 0
vallenderlab / rnaseq-tuxedo-suite
An RNASeq snakemake workflow using the Tuxedo suite.
rnaseq-tuxedo rnaseq-pipeline rna-seq-pipeline rna-seq-snakemake snakemake snakemake-workflow
Language:Python 0
czheluo / circRNA
Predict circRNA pipeline
rnaseq-pipeline circrna circrna-pipeline
Language:Perl
kfarleigh / ResearchersGuideToPopulationGenomics
A book that discusses topics and contains tutorials relevant to population genomics
population-genetics population-genomics rnaseq rnaseq-analysis rnaseq-pipeline
Language:HTML

rnaseq-pipeline

Novartis / pisces

amarinderthind / RNA-seq-tutorial-for-gene-differential-expression-analysis

sunyumail93 / PipeRNAseq

eandresleon / miARma-seq

ajitjohnson / arseq

umccr / RNAsum

CGAT-Group / DICAST

czheluo / lncRNA-pipeline

LieberInstitute / SPEAQeasyWorkshop2020

mppl1 / RNAseq_preprocessing

kicheolkim / RNAseq_FullTx

jvandinter / container_pilot

LBGC-CFB / LoRID

milescsmith / rnaseq_pipeline

nbay13 / toilkit

PavlidisLab / rnaseq-variant-pipeline

sevdarafatov / RNASeq_snakemake

tdayris-perso / rna-count-salmon

WestGermanGenomeCenter / circrna_detection

Alruta / Kallisto-DESeq2_Pipeline

CreedxAsif / Flowchart

kiranfranklin999 / Nextflow_tutorials

michalbukowski / rnaseq-pipeline-1

MJBioInfo / SnakemakeWorkflow

simon-bt / sm-rnaseq-splicing

sup1496 / RNASeq-Analysis

vallenderlab / rnaseq-tuxedo-suite

czheluo / circRNA

kfarleigh / ResearchersGuideToPopulationGenomics