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perl-bio-tools-run-alignment-clustalw
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public |
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
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2023-06-16 |
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perl-bio-coordinate
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public |
Methods for dealing with genomic coordinates.
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2023-06-16 |
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perl-bio-tools-run-alignment-tcoffee
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public |
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
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2023-06-16 |
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xhmm
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public |
XHMM (eXome-Hidden Markov Model).
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2023-06-16 |
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perl-test-requiresinternet
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public |
Easily test network connectivity
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2023-06-16 |
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centroid_rna_package
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public |
Collection of RNA secondary structure prediction programs based on gamma-centroid estimator (Hamada et. al. 2009)
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2023-06-16 |
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novasplice
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public |
NovaSplice is a python tool to predict novel intronic splice sites from a given VCF file
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2023-06-16 |
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perl-graphics-colorobject
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public |
convert between color spaces
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2023-06-16 |
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perl-graphics-colornames
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public |
defines RGB values for common color names
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2023-06-16 |
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perl-test-memory-cycle
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public |
Verifies code hasn't left circular references
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2023-06-16 |
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perl-devel-cycle
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public |
Find memory cycles in objects
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2023-06-16 |
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perl-module-loaded
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public |
Mark modules as loaded/unloaded
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2023-06-16 |
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phantompeakqualtools
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public |
This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
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2023-06-16 |
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deepsvr
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public |
DeepSVR stands for deep somatic variant refinement. It uses deep learning to classify real somatic and anomalous variants in paired tumor sequencing data.
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2023-06-16 |
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deepbinner
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public |
A signal-level demultiplexer for Oxford Nanopore reads.
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2023-06-16 |
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wes-service-client
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public |
Implementation of the GA4GH Workflow Execution Service, a REST service for running workflows; client support only
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2023-06-16 |
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pbcoretools
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public |
CLI tools and add-ons for PacBio's core APIs
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2023-06-16 |
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convert_zero_one_based
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public |
Convert between zero and one based coordinate systems
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2023-06-16 |
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r-coenocliner
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public |
Simulate species occurrence and abundances (counts) along gradients.
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2023-06-16 |
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r-rebird
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public |
A programmatic client for the eBird database, including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
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2023-06-16 |
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r-ggrasp
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public |
Given a group of genomes and their relationship with each other, the package clusters the genomes and selects the most representative members of each cluster. Additional data can be provided to the prioritize certain genomes. The results can be printed out as a list or a new phylogeny with graphs of the trees and distance distributions also available. For detailed introduction see: Thomas H Clarke, Lauren M Brinkac, Granger Sutton, and Derrick E Fouts (2018), GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models, Bioinformatics, bty300, <doi:10.1093/bioinformatics/bty300>.
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2023-06-16 |
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r-bipartite
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public |
Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
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2023-06-16 |
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r-spocc
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public |
A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
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2023-06-16 |
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perl-cache-cache
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public |
extends Cache::SizeAwareMemoryCache
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2023-06-16 |
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pblaa
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public |
PacBio tool to deconvolute mixtures of alleles and loci into phased consensus sequences.
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2023-06-16 |
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r-rgbif
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public |
A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; <https://www.gbif.org/developer/summary>). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge amounts of data.
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2023-06-16 |
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r-phylosignal
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public |
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
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2023-06-16 |
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krocus
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public |
krocus performs multi-locus sequence typing from uncorrected long reads.
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2023-06-16 |
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biopet-validateannotation
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public |
ValidateAnnotationvalidates whether an annotation file is correct.
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2023-06-16 |
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sourcetracker
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public |
Python implementation of the SourceTracker R package.
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2023-06-16 |
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advntr
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public |
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
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2023-06-16 |
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perl-package-stash-xs
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public |
faster and more correct implementation of the Package::Stash API
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2023-06-16 |
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plascope
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public |
PlaScope is a targeted approach to assess the plasmidome of bacteria.
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2023-06-16 |
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perl-json-pp
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public |
JSON::XS compatible pure-Perl module.
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2023-06-16 |
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perl-cpan-meta-yaml
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public |
Read and write a subset of YAML for CPAN Meta files
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2023-06-16 |
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ssake
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public |
SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences.
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2023-06-16 |
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perl-class-singleton
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public |
Base class for creating singleton objects
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2023-06-16 |
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bamclipper
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public |
Remove primer sequence from BAM alignments by soft-clipping.
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2023-06-16 |
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perl-version
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public |
Structured version objects
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2023-06-16 |
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arboreto
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public |
Scalable gene regulatory network inference using tree-based ensemble regressors
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2023-06-16 |
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mauve
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public |
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion
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2023-06-16 |
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barriers
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public |
Compute local minima and energy barriers of a landscape.
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2023-06-16 |
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perl-text-abbrev
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public |
abbrev - create an abbreviation table from a list
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2023-06-16 |
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phyluce
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public |
Software for UCE (and general) phylogenomics.
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2023-06-16 |
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perl-storable
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public |
persistence for Perl data structures
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2023-06-16 |
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sshmm
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public |
ssHMM is an RNA motif finder that recovers sequence-structure motifs from RNA-binding protein data, such as CLIP-Seq data.
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2023-06-16 |
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tardis
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public |
Pre-processor for bioinformatics cluster job submission
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2023-06-16 |
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gbsx
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public |
Toolkit for experimental design and demultiplexing genotyping by sequencing experiments
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2023-06-16 |
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icount
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public |
Computational pipeline for analysis of iCLIP data
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2023-06-16 |
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biopet-basecounter
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public |
BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.
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2023-06-16 |
