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-pipelinernaseq-pipelinetranscriptomicssalmonbioinformaticsrnaseq
  Language:Python 28

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

  This tutorial is created for educational purpose

  rnaseq-pipelinernaseqrnaseq-workshopdeseq2edgerenrichment-analysisbioconductor-packagesreactome-pathwaypca-analysisrna-seq-dgetutorialgene-expressionanalysisrna-seqrngsngs-analysis
  Language:R 27

• sunyumail93 / PipeRNAseq

  A comprehensive pipeline for RNAseq data analysis

  rnaseq-pipelinetranscriptome-analysisbioinformaticsrnaseqbioinformatics-analysisbioinformatics-pipelinegene-expressionrnarna-seq-analysisrna-sequencing
  Language:Shell 21

• eandresleon / miARma-seq

  miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis

  rnaseq-pipelinerna-seq-analysismirnamirna-seqcircrna-pipeline
  Language:Perl 13

• ajitjohnson / arseq

  An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)

  rna-seq-analysisrnaseq-pipelinerna-seqrnaseq
  Language:R 9

• umccr / RNAsum

  Pipeline for generating RNAseq-based cancer patient reports

  rnaseq-reportrnaseq-pipeline
  Language:R 7

• CGAT-Group / DICAST

  Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.

  transcriptomicsrnaseq-pipelinernaseq-analysisdockersnakemake
  Language:Python 6

• czheluo / lncRNA-pipeline

  lncRNA analysis pipeline

  lncrna-pipelinernaseq-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/.

  rstatsspeaqeasybioconductorlimmarnaseq-pipelinenextflownextflow-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

  differential-gene-expressionhisat2rnaseq-pipelinestringtietranscriptome-assembly
  Language:Shell 3

• kicheolkim / RNAseq_FullTx

  RNA-Seq data analysis: whole transcriptome, stranded, dUTP method

  rna-seqrna-seq-analysisrna-sequencingrnaseqrnaseq-pipeline
  Language:R 2

• jvandinter / container_pilot

  pilot pipeline that includes tool containerization

  ribosome-profilingrnaseq-pipeline
  Language:Shell 1

• LBGC-CFB / LoRID

  Long Read Isoform Discovery tool

  longreadrnaseq-pipeline
  Language:Python 1

• milescsmith / rnaseq_pipeline

  Snakemake+singularity RNAseq processing pipeline

  rnaseqrna-seqrnaseq-pipelinepipelinesnakemakebioinformatics-pipelinebioinformaticsnextflow
  Language:Python 1

• nbay13 / toilkit

  A python package for working with inputs to and outputs from the toil-rnaseq pipeline

  rnaseq-pipelinetranscriptomicsbioinformaticsrnaseqrsemfastqcsequence-alignment
  Language:Python 1

• PavlidisLab / rnaseq-variant-pipeline

  Pipeline for calling and analyzing variants from RNA-Seq data

  gatk4picardstarrnaseq-pipelinevariant-callingluigi-workflowsrnaseq
  Language:Python 1

• sevdarafatov / RNASeq_snakemake

  These snakefiles are prepared for the snakemake pipeline for the RNASeq analysis

  pythonrnaseq-pipelinesnakemake
  Language:Python 1

• tdayris-perso / rna-count-salmon

  Snakemake workflow for Salmon quantification and FastQC quality controls

  snakemake-workflowsbioinformatics-pipelinereproducible-workflowsrnaseq-pipelinefastqcsalmonmultiqc
  Language:Python 1

• WestGermanGenomeCenter / circrna_detection

  circs_snake : a snakemake-based circRNA detection workflow

  circularrnarna-seqrna-seq-pipelinernaseq-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 :)

  deseq2deseq2-analysiskallistorrstudiorna-seqrnaseq-analysisrnaseq-pipeline
  0

• CreedxAsif / Flowchart

  This Repository contains various Flowcharts, Visual and Graphical representations which are all created for educational purposes

  diagramseducationelisaelisa-resultsflowchartrnaseq-pipeline
  0

• kiranfranklin999 / Nextflow_tutorials

  Introduction to Bioinformatics workflows with Nextflow

  nextflowrnaseqrnaseq-pipeline
  Language:Nextflow 0

• michalbukowski / rnaseq-pipeline-1

  Simple Snakemake RNA-Seq pipeline

  rna-seqrnaseq-analysisrnaseq-pipelinedgedge-analysispython3rsnakemakesnakemake-pipelinesnakemake-rna-seqsalmonsalmon-deseq2pandasbioconductorminicondapythonminiconda3
  Language:Python 0

• MJBioInfo / SnakemakeWorkflow

  In this repository : i have created RNAseq pipeline using snakemake rules

  rnaseq-pipelinesnakemake-workflow
  Language:Python 0

• simon-bt / sm-rnaseq-splicing

  Snakemake pipeline for alternative slicing analysis with VAST-TOOLS

  alternative-splicingrnaseq-analysisrnaseq-pipelinesnakemake-workflowvast-tools
  Language:Python 0

• sup1496 / RNASeq-Analysis

  A basic pipeline for the analysis of RNASeq data. Entirely done in Bash and R script.

  bash-scriptrrnaseq-pipeline
  Language:Shell 0

• vallenderlab / rnaseq-tuxedo-suite

  An RNASeq snakemake workflow using the Tuxedo suite.

  rnaseq-tuxedornaseq-pipelinerna-seq-pipelinerna-seq-snakemakesnakemakesnakemake-workflow
  Language:Python 0

• czheluo / circRNA

  Predict circRNA pipeline

  rnaseq-pipelinecircrnacircrna-pipeline
  Language:Perl

• kfarleigh / ResearchersGuideToPopulationGenomics

  A book that discusses topics and contains tutorials relevant to population genomics

  population-geneticspopulation-genomicsrnaseqrnaseq-analysisrnaseq-pipeline
  Language:HTML