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bioconda-recipes

Conda recipes for the bioconda channel.

charlotteanne

clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

edition-jekyll-template

:books: Product documentation template for Jekyll

getfasta_nf

nextflow pipeline to get fastas

labranchor

LaBranchoR predicts RNA splicing branchpoints using a LSTM network. LaBranchoR uses only the sequence 1 to 70 base pairs upstream of a three prime splice site as a feature. In our paper, we show that LaBranchoR predicts a correct branchpoint for over 90% of 3' splice sites! See our website for precomputed predictions for all introns in gencode v19.

m6aboost

modules

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

mscthesis

A collection of scripts for my Bioinformatics MSc thesis

pub_scripts

resolve-nanopore-duplex

After duplex calling using Guppy you are left with a fastq of duplexes and one of simplexes - this script takes both and the list of paired reads to create one final file where there is not duplication of reads.

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

test-datasets

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

umicollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.