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rna-seq-analysis

rna-seq-analysis-bombus-bee

rna-seq-analysis-of-bombus-bee

rnaseq-nf

A proof of concept of RNAseq pipeline

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scikit-lego

Extra blocks for scikit-learn pipelines.

see

:art: Visualisation toolbox for beautiful and publication-ready figures

shiny

Various Shiny applications.

shinycopynumber

test app to get copy number variation information

sigr2021

simulans_transposable

sircovid

sistr_cmd

SISTR (Salmonella In Silico Typing Resource) command-line tool

small-plasmid-nanopore

snakemake

High throughput Next Generation Sequencing (NGS) data analysis using Python 3 Snakemake

snakemake-1

This is the development home of the workflow management system Snakemake. For general information, see

sqlmodel

SQL databases in Python, designed for simplicity, compatibility, and robustness.

star

RNA-seq aligner

staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

stringtie

Transcript assembly and quantification for RNA-Seq

sunday_streams

Code for all of my Sunday streams (https://www.twitch.tv/kierisi), focused primarily on machine learning using the {tidymodels} framework

telr

TELR is a fast non-reference transposable element detector from long read sequencing data.

treeviewer

Cross-platform software to draw phylogenetic trees

trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

tutorials

Tutorials on how to use the microGVL to do common bacterial bioinformatic tasks

umicountr

vcf-analysis

VCF analysis of Plasmodium falciparum SNPs, MOI, and phylogeny.

vcf-kit

VCF-kit: Assorted utilities for the variant call format

whatlies

Toolkit to help understand "what lies" in word embeddings. Also benchmarking!

xdm

Powerfull download accelerator and video downloader