Discover @wwood Open Source projects

Ben J Woodcroft (@wwood)

wwood

Stars
695
Global Rank 41,856 (Top 2 %)
Followers 210
Following 40
Registered almost 16 years ago
Most used languages

Ruby
64.5 %

Python
11.3 %

Rust
11.3 %

C
4.8 %

Jupyter Notebook
3.2 %

Perl
1.6 %

JavaScript
1.6 %

Shell
1.6 %
Location 🇦🇺 Australia
Country Total Rank 746
Country Ranking

Rust
38

Ruby
124

Perl
177

Python
197

C
409

Jupyter Notebook
660

Shell
1,596

JavaScript
7,942

CoverM

Read coverage calculator for metagenomics

kingfisher-download

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

singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes

galah

More scalable dereplication for metagenome assembled genomes

OrfM

simple and not slow ORF caller

goruby

Gene Ontology (GO) interface for Ruby

rarff

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

bbbin

A collection of working and non-working bioinformatics scripts

finishm

genome improvement and finishing without further sequencing effort

bioruby-kmer_counter

A biogem for counting small kmers for fingerprinting nucleotide sequences

bioruby-cigar

A parser for CIGAR format alignments

bioruby-sra

Ruby interface to the NCBI Sequence Read Archive (SRA)

scim

(Unofficial) Smart Common Input Method

bacterial_dating_aerobic_predictor

Prediction of aerobicity in extant and ancient genomes

Jupyter Notebook

excelsior

NO LONGER MAINTAINED.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

smafa

Biological sequence aligner for pre-aligned sequences

bioruby-signalp

A wrapper for the signal peptide prediction algorithm SignalP

dirseq

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

bioruby-ipcress

Parser for the ipcress in-silico PCR program

hmmer-rs

Ergonomic Rust interface to HMMER

bioruby-tm_hmm

A bioruby plugin for interaction with the transmembrane predictor TMHMM

bioruby-orthomcl

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

ace2sam

(fork) Converts an ACE alignment to a SAM file

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.

bioruby-hmmer3_report

Parser for hmmsearch and hmmscan in the HMMER 3 package.

bird_tool_utils-rust

Utility functions for the bird metagenomic toolkit

bioruby-pileup_iterator

Iterate through a samtools pileup file

eupathdb_ubiquity

EuPathDB Ubiquity scripts

bioruby-stockholm

Parser for stockholm format files

exportpred

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

blast_link

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

reach

Extend the Ruby Array class for less loops and blocks

bioruby-cnls_screenscraper

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

wwood.github.com

reubypathdb

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

checkm-rs

Rust library for CheckM genome assessor

mfqe

FASTA/FASTQ extractor for multiple sets of read names

bioruby-cog_categories

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

ApiLocServer

The web interface behind the ApiLoc server

singlem_host_or_ecological_predictor

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

bird_tool_utils-python

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

ApiLoc

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

essentiality

Finding patterns to predict the essentiality of genes

biouby-agp

A Ruby parser of AGP format assembly scaffolding files

tree2tax

Automatic taxonomy through consistent application of tree-based thresholding

bioruby-octopus

Running and parsing of the protein transmembrane domain predictor octopus

bioruby-hmmer_model

Parse PFAM HMM definition files

vietnamese_mnemosyne

A deck of memory flash cards from learning Vietnamese

bioruby-krona

Programmatic interface to krona visualisations

bioruby-newbler_outputs

Parsers for outputs from the assembly program Newbler

extern

Convenient python shell command running library

bioruby-exportpred

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

bioruby-wolf_psort_wrapper

Enables the localisation predictor WoLF PSORT to be run locally

ben_bioinformatics

A collection of random bioinformatic rails plugin

bioruby-aliphatic_index

TODO: one-line summary of your gem

bioruby-hydropathy

Hydropathy scale for BioRuby

yargraph

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

SilkSlider

Predict silk-like proteins

tree2tax2

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

bioruby-plasmoap

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

bioruby-sra_fastq_dumper

Programmatically use the fastq-dumper tool from the SRA toolkit

array_pair

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

amplicon_encyclopaedia

TODO: one-line summary of your gem

bioruby-img_database

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

singlem-benchmarking

Jupyter Notebook

bioruby-emboss_six_frame_nucleotide_sequences

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