| 1 | 43,118 | 27,037 | bio-velvet | Parser to work with some file formats used in the velvet DNA assembler |
| 2 | 43,918 | 41,737 | bio-tm_hmm | A bioruby plugin for interaction with the transmembrane predictor TMHMM |
| 3 | 45,482 | 41,737 | bio-signalp | A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, ... |
| 4 | 45,661 | 41,737 | bio-commandeer | A dead simple method of running shell commands from within Ruby, by applying opinion |
| 5 | 46,465 | 94,007 | bio-kmer_counter | A biogem for counting small kmers for fingerprinting nucleotide sequences. See README f... |
| 6 | 51,209 | 74,024 | finishm | De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving ... |
| 7 | 52,139 | 61,331 | wwood-rarff | Rarff is a Ruby library for dealing with Attribute-Relation File Format (ARFF) files. A... |
| 8 | 54,594 | 46,531 | divvy_proteomics | divvy up spectra from DTASelect files in a somewhat parsimonious way |
| 9 | 55,226 | 32,343 | bio-velvet_underground | Bindings to some internals of the velvet assembler. |
| 10 | 59,548 | 61,331 | wwood-reach | For instance, a ReachableArray of Book objects can not only take normal Array methods s... |
| 11 | 59,868 | 53,031 | dirseq | FPKG (gene expression metric) calculator for metatranscriptomics |
| 12 | 63,394 | 129,210 | bio-plasmoap | The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptid... |
| 13 | 63,999 | 74,024 | array_pair | random useful methods for working with Ruby arrays and hashes |
| 14 | 66,468 | 94,007 | bio-octopus | Running and parsing of the protein transmembrane domain predictor octopus |
| 15 | 66,806 | 46,531 | bio-krona | This biogem is built around Krona, a flashy way of representing hierarchical data. |
| 16 | 69,103 | 74,024 | bio-pileup_iterator | Iterate through a samtools pileup file |
| 17 | 69,737 | 61,331 | reubypathdb | Classes to help parsing EuPathDB data files |
| 18 | 72,474 | 94,007 | goruby | GoRuby makes it easy to interact with the Gene Ontology by using the infrastructure set... |
| 19 | 76,515 | 61,331 | bio-sra | A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA meta... |
| 20 | 77,523 | 94,007 | rarff | Library for handling Weka ARFF files |
| 21 | 80,253 | 61,331 | SilkSlider | Predict silk-like proteins from its amino acid sequence. |
| 22 | 88,166 | 94,007 | bio-wolf_psort_wrapper | Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is avail... |
| 23 | 90,757 | 74,024 | bio-hmmer_model | Parse PFAM HMM definition files so that the models can be accessible programmatically |
| 24 | 90,787 | 94,007 | bio-gag | bio-gag is a biogem for detecting and correcting a particular type of error that occurs... |
| 25 | 92,345 | 94,007 | yargraph | Pure Ruby graph algorithms, particularly e.g. Hamiltonian cycles |
| 26 | 95,395 | 129,210 | bio-hmmer3_report | Enables programmatic parsing of HMMER version 3 reports |
| 27 | 99,358 | 129,210 | bio-ipcress | a programmatic interface to the iPCRess in-silico PCR software. iPCRess is part of the ... |
| 28 | 100,673 | 74,024 | bio-cigar | A parser for CIGAR format alignments. |
| 29 | 101,088 | 129,210 | bio-express_beta_diversity | Interface for express beta diversity file formats |
| 30 | 104,652 | 129,210 | img_scripts | Scripts related to the IMG (Integrated Microbial Genomes) database |
| 31 | 118,677 | 129,210 | bio-emboss_six_frame_nucleotide_sequences | a method to get the nucleotide sequence of translations done by the EMBOSS bioinformati... |
| 32 | 119,222 | 94,007 | bio-exportpred | Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins.... |
| 33 | 121,025 | 94,007 | bio-hydropathy | Hydropathy scale for BioRuby |
| 34 | 121,136 | 129,210 | bio-aliphatic_index | A simple biogem that allows computation of the aliphatic index of a protein |
| 35 | 123,720 | 94,007 | bio-stockholm | Parses stockholm sequence alignment format |
| 36 | 125,196 | 129,210 | bio-img_metadata | Reads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmat... |
| 37 | 137,240 | 94,007 | reachable | For instance, a ReachableArray of Book objects can not only take normal Array methods s... |
| 38 | 167,266 | 129,210 | bio-primer3 | Primer3-related Ruby code - wrappers, Boulder IO, etc. |
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