rna-seq-pipeline

There are 5 repositories under rna-seq-pipeline topic.

RNAlysis
GuyTeichman / RNAlysis
RNA sequencing analysis software
rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna smallrna-seq gui-application
Language:Python 121
urmi-21 / pyrpipe
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
rna-seq rna-seq-pipeline ncbi-sra bioinformatics bioinformatics-pipeline bioinformatics-analysis python rna-seq-workflows conda bioconda
Language:Python 78
uc-bd2k / GREIN
GREIN : GEO RNA-seq Experiments Interactive Navigator
rna-seq geo bioinformatics-pipeline bioinformatics-analysis rna-seq-pipeline rna-seq-data rna-seq-analysis graphical-interface r shiny-apps gene-expression-omnibus interactive-visualizations interactive-analysis processing geo-data-processing grein gene-expression
Language:HTML 48
jumphone / SPRINT
SNP-free RNA editing Identification Toolkit
rna-seq-analysis rna-editing rna-seq rna-seq-pipeline rna-seq-mapping
Language:Python 42
gaolabtools / scNanoGPS
Single cell Nanopore sequencing data for Genotype and Phenotype
cell-barcode demultiplexing gene-expression isoforms long-read-sequencing nanopore-analysis-pipeline rna-seq-pipeline single-cell single-nucleotide-variation umi-curation
Language:Python 33
Taiji-pipeline / Taiji
All-in-one analysis pipeline
atac-seq-pipeline rna-seq-pipeline single-cell-atac-seq single-cell-rna-seq transcriptional-regulatory-network
Language:Haskell 33
NCBI-Hackathons / SPeW
Automatic Packaging and Distribution of Bioinformatics Pipelines
pipeline nextflow docker rna-seq-pipeline
Language:Python 26
PalMuc / TransPi
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
rna-seq-pipeline denovo-assembly non-model-species rna-seq transcriptomics assembly annotation nextflow nextflow-pipeline
Language:Nextflow 26
giuliospinozzi / arpir
Automatic RNA-Seq Pipelines with Interactive Report
rna-seq rna-seq-pipeline rna-seq-analysis report-generator automated
Language:R 25
uc-bd2k / GREP2
GEO RNA-seq Experiments Processing Pipeline
rna-seq gene-expression-omnibus sratoolkit sra pipeline rna-seq-pipeline
Language:R 20
egaffo / CirComPara
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
bioinformatics-pipeline bioinformatics rna-seq circrna rna-seq-data rna-seq-analysis rna-seq-pipeline gene-expression circrnas circular-rna transcriptomics circseq
Language:R 14
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)
bioinformatics snakemake rna-seq-analysis rna-seq-pipeline genomics conda docker
Language:Python 12
eonurk / RNA-seq-differential-analyses-guideline
A quick recap of widely used differential analyses methods in R for RNA-seq experiments
edger deseq2 limma limma-voom limma-trend rna-seq-pipeline
12
apredeus / multi-bacpipe
A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments
rna-seq-analysis rna-seq rna-seq-pipeline bacteria
Language:Perl 9
schosio / CHOLAR
Automated RNA-seq pipeline for lncRNA indentification
automated lncrna lncrna-pipeline rna-seq-analysis rna-seq-pipeline lncrna-identification bioinformatics
Language:Shell 9
zqfang / snakeflow
bioinfo workflow based on snakemake
rna-seq-pipeline atac-seq-pipeline
Language:Python 9
cellgeni / rnaseq
Fast RNAseq pipeline
rna-seq-pipeline nextflow
Language:Groovy 8
hanielcedraz / BAQCOM
Quality Control, Mapping and Reads Count for RNA-Seq Analysis
trimmomatic star quality-control rna-seq-analysis rna-seq-pipeline mapping rnaseqpipeline rna-seq-mapping rna-seq-qc bioinformatics bioinformatics-pipeline rna-seq-aligner multiqc fastqc hisat2 htseq-count featurecounts
Language:R 8
HKU-BAL / Clair3-RNA
Clair3-RNA - a long-read small variant caller for RNA sequencing data
deep-learning long-read-sequencing nanopore ont pacbio-iso-seq rna rna-editing rna-seq rna-seq-pipeline variant-calling
Language:Python 8
LappalainenLab / RNApipeline
rna-seq pipeline rna-seq-pipeline
Language:Shell 8
czheluo / Teach-Bioinformatics-R-dataviz
Materials for "Teaching Bioinformatics and R for dataviz course" June-August 2019 in Majorbio
dataviz rna-seq-pipeline teaching-bioinformatics teaching-statistics
Language:R 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
rna-seq-pipeline rna-seq-analysis slurm rawreads fastq sortmerna
Language:HTML 7
zavolanlab / PAQR2
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
bioinformatics snakemake rna-seq-pipeline polyadenylation
Language:Python 7
Lexogen-Tools / quantseqpool_analysis
Standard analysis routine for samples that were generated with Lexogen's QuantSeq pool library preparation kit.
rna-seq-pipeline quantseq quantseqpool
Language:Shell 6
DKFZ-ODCF / RNAseqWorkflow
Roddy RNA-seq Workflow Plugin
roddy bioinformatics-pipeline rna-seq-pipeline rna
Language:Perl 5
EmoryIntegratedComputationalCore / Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
qiime2 microbiome-analysis rna-seq-analysis rna-seq-pipeline deseq2 phyloseq ldm omics-experiments emory methods rna-seq bioconductor bayseq edger qvalue discovery-rates comparison-groups notebook analytical-processes
Language:R 5
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
rna-seq-pipeline snakemake differential-gene-expression reproducible-research r python
Language:R 5
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.
rstats rnaseq nextflow pipeline hisat2 speaqeasy rna-seq-pipeline
Language:HTML 5
mhjiang97 / RNASeqFlow
A small python tool for RNA-seq workflows
python rna-seq-pipeline workflow
Language:Python 5
yuragal / fradians-rnaseq
De nove assembly and annotation of Fragilaria radians transcriptome
rna-seq-pipeline protists transcriptome assembly annotation
Language:R 5
pentalpha / r-peridot
Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.
differential-expression differential-expression-analysis gene-expression rna-seq-analysis rna-seq-pipeline bioinformatics bioinformatics-pipeline bioconductor bioinformatics-analysis bioinformatics-tool
Language:Java 4
pentalpha / r-peridot-gui
The power of the R's differential gene expression analysis packages, with no programming required.
bioinformatics bioinformatics-pipeline bioinformatics-analysis gui-application differential-expression transcriptomics genomics rna-seq rna-seq-analysis rna-seq-pipeline
Language:Java 3
scienceforever / GLSeq
Pipeline for low-level RNA-Seq data processing
transcriptome rna-seq-pipeline r pipeline transcriptomics rna-sec bacterial-transcription rsem fastq
Language:R 3
sing-group / dewe
DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.
rna-seq rna-seq-pipeline rna-seq-data differential-expression aibench java
Language:Java 3
vivekruhela / miRPipe
miRPipe: Open source RNA-Seq bioinformatics analysis docker for identification of miRNAs and piRNAs
rna-seq-pipeline paralogs pirna docker
Language:Python 3
niekwit / rna-seq-star-tetranscripts
Snakemake workflow for transposable element RNA-Seq using TEtranscripts
ngs-pipeline rna-seq-pipeline snakemake-workflow transposable-elements
Language:R 2