nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Repository to host tool-specific module files for the Nextflow DSL2 community!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Converts bam or cram files to fastq format and does quality control.
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Precision HLA typing from next-generation sequencing data
Config files used to define parameters specific to compute environments at different Institutions
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.