mdchia

fast5_fetcher

A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

PlotsOfData

Shiny App for comparison of samples

MLDSP

Machine Learning with Digital Signal Processing

DAtest

Compare different differential abundance and expression methods

fastq_utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Easy-Leaf-Area

ggrastr

Raster geoms for ggplot2

rvg

HGTector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

DABEST-python

Data Analysis with Bootstrapped ESTimation

fastqe

FASTQ sequence quality visualisation with Emoji

POREquality

This is an early version of POREquality, an R Markdown document designed to be ran as part of a Nanopore local basecalling pipeline.

last-rna

powscript

transpiler written in bash: painless shellscript, indentbased, coffee for the shell with hipster-sparkles v1 BETA LANDED 🎉🎉🎉🎉 thanks fcard!

termtosvg

Record terminal sessions as SVG animations

ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

carrierseq

a sequence analysis workflow for low-input nanopore sequencing

poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing

circlize

Circular visualization in R

metagenomics-tutorials

Additional scripts from tutorials on tylerbarnum.com

partie

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

pullseq

Utility program for extracting sequences from a fasta/fastq file

Rcade

Games to procrastinate with RStudio

corgi

Corgi is a command-line workflow manager that helps with your repetitive command usages by organizing them into reusable snippet

phd_thesis_markdown

Template for writing a PhD thesis in Markdown

NGSPanPipe

Developing pangenome from NGS short-reads

drake

An R-focused pipeline toolkit for reproducibility and high-performance computing

PanPred

A library of Machine Learning tools to predict antibiotic resistance from NGS data

minion_qc

Quality control for MinION sequencing data