Auzbert's Gems

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#Total RankDaily RankNameSummary
143,74597,318bio-velvetParser to work with some file formats used in the velvet DNA assembler
244,84997,318bio-tm_hmmA bioruby plugin for interaction with the transmembrane predictor TMHMM
345,16755,892bio-commandeerA dead simple method of running shell commands from within Ruby, by applying opinion
446,40241,970bio-signalpA wrapper for the signal peptide prediction algorith SignalP. Not very well supported, ...
547,12755,892bio-kmer_counterA biogem for counting small kmers for fingerprinting nucleotide sequences. See README f...
651,95835,772finishmDe-novo assemblies generally only provide draft genomes. FinishM is aimed at improving ...
753,15197,318wwood-rarffRarff is a Ruby library for dealing with Attribute-Relation File Format (ARFF) files. A...
855,56755,892divvy_proteomicsdivvy up spectra from DTASelect files in a somewhat parsimonious way
955,81755,892bio-velvet_undergroundBindings to some internals of the velvet assembler.
1060,67735,772wwood-reachFor instance, a ReachableArray of Book objects can not only take normal Array methods s...
1160,77229,191dirseqFPKG (gene expression metric) calculator for metatranscriptomics
1264,45055,892bio-plasmoapThe PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptid...
1365,35397,318array_pairrandom useful methods for working with Ruby arrays and hashes
1467,60741,970bio-octopusRunning and parsing of the protein transmembrane domain predictor octopus
1567,75597,318bio-kronaThis biogem is built around Krona, a flashy way of representing hierarchical data.
1670,44741,970bio-pileup_iteratorIterate through a samtools pileup file
1771,13655,892reubypathdbClasses to help parsing EuPathDB data files
1873,89855,892gorubyGoRuby makes it easy to interact with the Gene Ontology by using the infrastructure set...
1977,50655,892bio-sraA Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA meta...
2079,00097,318rarffLibrary for handling Weka ARFF files
2181,48529,191SilkSliderPredict silk-like proteins from its amino acid sequence.
2289,70497,318bio-wolf_psort_wrapperEnables the localisation predictor WoLF PSORT to be run locally. The algorithm is avail...
2392,13997,318bio-gagbio-gag is a biogem for detecting and correcting a particular type of error that occurs...
2492,15697,318bio-hmmer_modelParse PFAM HMM definition files so that the models can be accessible programmatically
2593,49197,318yargraphPure Ruby graph algorithms, particularly e.g. Hamiltonian cycles
2696,55641,970bio-hmmer3_reportEnables programmatic parsing of HMMER version 3 reports
2799,76597,318bio-ipcressa programmatic interface to the iPCRess in-silico PCR software. iPCRess is part of the ...
28101,47597,318bio-cigarA parser for CIGAR format alignments.
29102,41697,318bio-express_beta_diversityInterface for express beta diversity file formats
30106,49835,772img_scriptsScripts related to the IMG (Integrated Microbial Genomes) database
31120,36141,970bio-emboss_six_frame_nucleotide_sequencesa method to get the nucleotide sequence of translations done by the EMBOSS bioinformati...
32120,84755,892bio-exportpredWrapper around the ExportPred algorithm for predicting P. falciparum exported proteins....
33122,72997,318bio-hydropathyHydropathy scale for BioRuby
34122,84997,318bio-aliphatic_indexA simple biogem that allows computation of the aliphatic index of a protein
35125,07241,970bio-stockholmParses stockholm sequence alignment format
36127,02955,892bio-img_metadataReads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmat...
37139,76755,892reachableFor instance, a ReachableArray of Book objects can not only take normal Array methods s...
38170,03997,318bio-primer3Primer3-related Ruby code - wrappers, Boulder IO, etc.