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analysis-isoseq

GENE-SWitCH project Iso-Seq analysis pipeline

bioconda-recipes

Conda recipes for the bioconda channel.

bioinfo-scripts

Personnal bioinfo scripts

bioinfo-utils

Scripts for bioinfo data analysis

densitymap

DensityMap is perl tool for the visualization of features density along chromosomes

differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

gs-tama

GENE SWitCH Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

isoseq

isoseq_v3-singularity

A definition file for building IsoSeq v3 singularity container

mixcr-singularity-container

A repo to store singularity version of mixcr docker image

multi-package-containers

Testing building mulled containers for multi-requirement tools.

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

multiqc_testdata

Test data for MultiQC. See https://github.com/ewels/MultiQC

nf-co.re

Code and files for the main nf-core website.

nf-core-isoseq

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

nf-core_modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nf-core_tools

Python package with helper tools for the nf-core community.

nf-feelnc

A simple nf script to run feelnc module (from FAANG/analysis-TAGADA)

nf-mixcr

A nextflow pipeline for TCR repertoire building with MiXCR

slamem

Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array

smrnaseq

A small-RNA sequencing analysis pipeline

sqanti3-singularity

A definition file for building SQANTI3 singularity container (adapted from [joelnitta/sqanti3-docker](https://github.com/joelnitta/sqanti3-docker))

strobemers

A repository for generating strobemers and evalaution

tama-docker

TAMA Dockerfile

tama-singularity

A definition file for building TAMA singularity container

test-datasets

Test data to be used for automated testing with the nf-core pipelines

ultra

uLTRA is a long-read splice aligner with high accuracy from using a guiding annotation