guigolab/gencode-cls-master-table

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guigolab/gencode-cls-master-table

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Results of the GENCODE pipeline to produce a collection of full length high quality transcripts

ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

grape-nf

An automated RNA-seq pipeline using Nextflow

FA-nf

Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow

bamstats

A command line tool to compute mapping statistics from a BAM file

geneidx

Nextflow pipeline for genome annotation of protein-coding genes

chip-nf

An automated ChIP-seq pipeline using Nextfow

LyRic

Long RNA-seq analysis workflow

geneid

Predict genic elements as splice sites, exons or genes, along eukaryotic DNA sequences

tmerge

Merge transcriptome read-to-genome alignments into non-redundant transcript models

CRISPETA

A really flexible tool to obtain CRISPR paired gRNAs on desired regions of a genome

sQTLseekeR2

R package to detect splicing QTLs (sQTLs)

ipsa-nf

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

sqtlseeker2-nf

An automated sQTL mapping pipeline using Nextflow

biogenome-portal

Biogenome data portal

sambamBench-nf

A simple Nextflow pipeline for testing the performance of sambamba vs samtools

DeepFryer

DeepFryer - Deep Learning Framework for Your Expression RNA-seq data

jbrowse-plugin-refget-api

A JBrowse 2 plugin to access servers implementing the refget API of GA4GH

pb_gen

Process PacBio Sequel and Sequel II subread BAMs into CCS FASTQ files