Project
Reverse Dependencies for bio
The projects listed here declare bio as a runtime or development dependency
0.0
Store relationships in a triple-store, such as gene enrichment and QTL, and use this information for inference and causality
2020
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0.0
Digests DNA based on restriction enzyme cut patterns
2020
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Provides PhyloXML support for BioRuby. This bioruby-phyloxml gem replaces old unmaintained bio-phyloxml gem.
2020
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0.0
New Sambamba library comes with a command-line tool for working with SAM/BAM files. This gem brings some of its functionality to Ruby.
2020
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0.0
Simple classes for parsing SAM, CIGAR and MD:Z strings, including slices. Methods for calling mutations in HGVS format and looking up consequences using Ensembl VEP REST API. Developed for calling mutations at an expected position in an alignment - e.g. Amplicon sequencing of CRISPR-induced mutat...
2020
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0.0
A minimal web service on the top of sinatra to query bam files
2020
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0.0
Wrapper of samtools for ruby.
This project was born from the need to add support of BAM files to
the gee_fu genome browser (http://github.com/danmaclean/gee_fu).
2020
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0.0
Entries in a flatfile will be parased by the BioRuby's Bio::FlatFile.auto module. These entries are used as queries for the Sun Grid Engine (SGE) system. Huge amount of queries are automatically splitted into subdirectories. With a specified command line to be executed, queries are submited to th...
2020
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0.0
BioRuby Shell is a command line interface on BioRuby open source bioinformatics library. It provides easy-to-use analysis environment for bioinformatics.
2020
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0.0
A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least.
2020
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A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.
2020
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Parses stockholm sequence alignment format
2020
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Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation.
2020
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0.0
A bioruby plugin for interaction with the transmembrane predictor TMHMM
2020
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BioRuby plugin for UniChem REST Web service
2020
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Parser to work with some file formats used in the velvet DNA assembler
2020
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Bindings to some internals of the velvet assembler.
2020
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Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/
2020
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a library and commandline tool to pick causative mutation from bulks segregant sequencing
2020
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FPKG (gene expression metric) calculator for metatranscriptomics
2020
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