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featurecounts

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bioinfo-notebook

rnnh /bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

bash bioinformatics ubuntu conda bioconda bash-script featurecounts video-demonstration fastq-dump windows-subsystem bioinformatics-programs bioinformatics-notebook

UpdatedNov 12, 2020
Shell

vivekbhr /Subread_to_DEXSeq

Scripts to import your FeatureCounts output into DEXSeq

rna-seq featurecounts dexseq

UpdatedOct 27, 2018
Python

bpucker /RNA-Seq_analysis

scripts for RNA-Seq analysis

python annotations gene-expression tpm rna-seq-analysis featurecounts gff count-table reference-genes fpkm

UpdatedFeb 20, 2022
Python

hanielcedraz /BAQCOM

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

bioinformatics quality-control mapping bioinformatics-pipeline multiqc star hisat2 rna-seq-analysis featurecounts rna-seq-mapping fastqc rna-seq-pipeline htseq-count rna-seq-qc rnaseqpipeline trimmomatic rna-seq-aligner

UpdatedMar 29, 2022
R

uhh-lt /lefex

A tool for extraction of lexical features from text based on UIMA and MapReduce

feature-extraction dependency-parser distributional-semantics extract-features featurecounts

UpdatedAug 24, 2018
Java

yejg2017 /Sequence-Mapping-Bio

This is a code tutorial for rna or dna sequence mapping by myself-RyanYip

multiqc star salmon htseq featurecounts bowtie2 fastqc

UpdatedDec 10, 2018
Shell

gih0004 /RNA_Seq_featurecounts

This repository contatins a pipeline for RNA-Seq data processing using featurecounts for gene count generation

rna-seq featurecounts

UpdatedMar 19, 2024
Shell

hernanmd /hisat2_bovine

Scripts to index and align Bovine genome with HISAT2

bash bioinformatics genome gff3 hisat2 featurecounts genome-alignment

UpdatedMay 22, 2018
Shell

Pinky-cloud224 /snakemake_workflow_rna_seq_data_analysis

config rna-seq jupyter-notebook conda python3 multiqc tpm salmon kallisto featurecounts paired-end fastq-files cutadapt fastqc htseq-count snakemake-workflow

UpdatedOct 20, 2022
Jupyter Notebook

bixBeta /atac

nextflow ATACseq pipeline for GG02

nextflow atac-seq homer featurecounts bowtie2

UpdatedMay 20, 2024
Nextflow

mattgalbraith /subread-docker-singularity

Build Docker container for Subread package and (optionally) convert to Apptainer/Singularity.

docker genomics sequencing singularity featurecounts apptainer subread

UpdatedMar 4, 2023
Dockerfile

monnieb92 /PROseq_Intron_Intergenic_Enhancers

A pipeline to call intron and intergenic eRNAs from PRO-seq Data

homer featurecounts macs2 pro-seq intronic ernas nrsa

UpdatedFeb 19, 2024
Shell

MaxGreil /rnaseq

Proof of concept of a RNA-Seq pipeline from reads to count matrix (including quality control) with Nextflow and additional example RNA-Seq analysis in R

docker bioinformatics quality-control rna-seq pipeline nextflow hisat2 rna-seq-analysis featurecounts rna-seq-pipeline

UpdatedJan 12, 2022
HTML

LeoooJR /ReproHackathon

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

shell bash cli r ubuntu nextflow hpc deseq2 google-cloud-platform samtools featurecounts bowtie ngs-analysis cutadapt ngs-pipeline fastqc sratoolkit apptainer

UpdatedDec 9, 2024
R

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