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1kgp_t2t_pangenie

bonito

Bonito - A PyTorch Basecaller for Oxford Nanopore Reads

fishpond

Differential transcript and gene expression, as well as helper functions for working with Salmon, alevin, and alevin-fry data

g2gtools

Personal diploid genome creation and coordinate conversion

leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

modules

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

nextflow

A DSL for data-driven computational pipelines

pangenie

Incorporating pre/post variant filtering when aligning to reference pangenomes

personalized_rnaseq

phasing_t2t

Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.

pimaker

Tool to calculate nucleotide diversity statistics in large pooled population datasets

qtlmap

Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

rnaseq

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

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

statannot

add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot

statannotations

add statistical annotations (pvalue significance) on existing boxplot/barplot generated by seaborn

taiyaki

Training models for basecalling Oxford Nanopore reads

tensorqtl_susie_suff_stats

Ultrafast GPU-based QTL mapper

vcfclass