Discover wwood/extern Open Source project by Ben J Woodcroft (@wwood)

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

300

kingfisher-download

Novelty-inclusive microbial community profiling of shotgun metagenomes

244

singlem

More scalable dereplication for metagenome assembled genomes

galah

simple and not slow ORF caller

OrfM

goruby

Gene Ontology (GO) interface for Ruby

(fork) A Ruby library for handling ARFF files, as popularized by the WEKA machine learning program

rarff

A collection of working and non-working bioinformatics scripts

bbbin

Prediction of aerobicity in extant and ancient genomes

bacterial_dating_aerobic_predictor

Jupyter Notebook

finishm

genome improvement and finishing without further sequencing effort

A biogem for counting small kmers for fingerprinting nucleotide sequences

bioruby-kmer_counter

A parser for CIGAR format alignments

bioruby-cigar

Ruby interface to the NCBI Sequence Read Archive (SRA)

bioruby-sra

(Unofficial) Smart Common Input Method

scim

smafa

Biological sequence aligner for pre-aligned sequences

NO LONGER MAINTAINED. Ruby gem that uses C bindings to read CSV files superfast. I'm totally serial!

excelsior

bioruby-signalp

A wrapper for the signal peptide prediction algorithm SignalP

Work out whether RNAseq reads in general agree with the direction of the gene predicted

dirseq

Parser for the ipcress in-silico PCR program

bioruby-ipcress

Ergonomic Rust interface to HMMER

hmmer-rs

A bioruby plugin for interaction with the transmembrane predictor TMHMM

bioruby-tm_hmm

Ruby wrappings and useful methods for the OrthoMCL database of protein orthology

bioruby-orthomcl

(fork) Converts an ACE alignment to a SAM file

ace2sam

bioruby-gag

bio-gag is a biogem for detecting and correcting a particular type of error (gag errors) that occurs/occurred in a particular version of the IonTorrent sequencing kit.

Parser for hmmsearch and hmmscan in the HMMER 3 package.

bioruby-hmmer3_report

Utility functions for the bird metagenomic toolkit

bird_tool_utils-rust

Iterate through a samtools pileup file

bioruby-pileup_iterator

EuPathDB Ubiquity scripts

eupathdb_ubiquity

bioruby-cnls_screenscraper

a bioruby plugin for interaction with the cNLS (classical Nuclear Localisation Signal) predictor

Parser for stockholm format files

bioruby-stockholm

(fork) fixes compilation errors in this predictor of P. falciparum exported proteins

exportpred

Shell

blast_link

A few scripts for turning a vanilla NCBI wwwblast installation into a link filled paradise.

Perl

reach

Extend the Ruby Array class for less loops and blocks

Website / continuous DB builds for SingleM

wwood.github.com

Personal Pages

sandpiper

Jupyter Notebook

reubypathdb

Ruby classes for parsing EuPathDB database download files from PlasmoDB, ToxoDB, CryptoDB, TriTrypDB, PiroplasmaDB and FungiDB, etc.

Opinionated Python utilities used in the bird suite of bioinformatic tools, developed by the Woodcroft lab

bird_tool_utils-python

Rust library for CheckM genome assessor

checkm-rs

FASTA/FASTQ extractor for multiple sets of read names

mfqe

API to Clusters of Orthologous Groups of proteins (COGs) functional categories

bioruby-cog_categories

The web interface behind the ApiLoc server

ApiLocServer

Predict whether a metagenome is from a host-associated sample or not based on its SingleM profile

singlem_host_or_ecological_predictor

Finding patterns to predict the essentiality of genes

essentiality

JavaScript

biouby-agp

A Ruby parser of AGP format assembly scaffolding files

Automatic taxonomy through consistent application of tree-based thresholding

tree2tax

A curated database of protein sub-cellular localisation in apicomplexan parasites

ApiLoc

Parse PFAM HMM definition files

bioruby-hmmer_model

Programmatic interface to krona visualisations

bioruby-krona

Parsers for outputs from the assembly program Newbler

bioruby-newbler_outputs

Running and parsing of the protein transmembrane domain predictor octopus

bioruby-octopus

Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins

bioruby-exportpred

A collection of random bioinformatic rails plugin

ben_bioinformatics

A deck of memory flash cards from learning Vietnamese

vietnamese_mnemosyne

bioruby-wolf_psort_wrapper

Enables the localisation predictor WoLF PSORT to be run locally

TODO: one-line summary of your gem

bioruby-aliphatic_index

Hydropathy scale for BioRuby

bioruby-hydropathy

Another Ruby graph (in the nodes and edges sense of the word) library

yargraph

Predict silk-like proteins

SilkSlider

Assign branch-length based taxonomy to trees free from the 7 levels

tree2tax2

Ruby implementation of the PlasmoAP program to predict apicoplast transit peptides in Plasmodium falciparum

bioruby-plasmoap

Run prodigal on microbial genomes automatically choosing between translation tables 4 and 11.

prodigal-runner

Containerised testing of SingleM installation methods

singlem-installation

Shell

array_pair

random useful methods for working with Ruby arrays, hashes and objects

Programmatically use the fastq-dumper tool from the SRA toolkit

bioruby-sra_fastq_dumper

TODO: one-line summary of your gem

amplicon_encyclopaedia

An activerecord-based offline database mirroring the Integrated Microbial Genomes (IMG) resource

bioruby-img_database

a method to get the nucleotide sequence of translations done by the EMBOSS bioinformatics package program transeq

singlem-benchmarking

Jupyter Notebook

bioruby-emboss_six_frame_nucleotide_sequences