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perl-module-util
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public |
Module name tools and transformations
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2023-06-16 |
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perl-env
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public |
perl module that imports environment variables as scalars or arrays
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2023-06-16 |
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r-seurat
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public |
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
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2023-06-16 |
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perl-getopt-long-descriptive
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public |
Getopt::Long, but simpler and more powerful
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2023-06-16 |
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perl-file-pushd
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public |
change directory temporarily for a limited scope
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2023-06-16 |
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super-focus
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public |
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
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2023-06-16 |
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perl-test-cleannamespaces
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public |
Check for uncleaned imports
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2023-06-16 |
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plasflow
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public |
PlasFlow - predicting plasmid sequences in metagenomic data
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2023-06-16 |
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minorseq
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public |
Minor Variant Calling and Phasing Tools
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2023-06-16 |
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perl-module-runtime-conflicts
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public |
Provide information on conflicts for Module::Runtime
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2023-06-16 |
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chado-tools
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public |
Tools to access CHADO databases
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2023-06-16 |
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gffmunger
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public |
Munges GFF3 files exported from Chado database to make them suitable for loading into WebApollo
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2023-06-16 |
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methylextract
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public |
High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
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2023-06-16 |
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perl-test-needs
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public |
Skip tests when modules not available
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2023-06-16 |
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perl-mro-compat
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public |
mro::* interface compatibility for Perls < 5.9.5
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2023-06-16 |
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perl-package-deprecationmanager
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public |
Manage deprecation warnings for your distribution
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2023-06-16 |
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perl-compress-bgzf
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public |
Read/write blocked GZIP (BGZF) files
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2023-06-16 |
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ditasic
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public |
DiTASiC is designed as a comprehensive approach for abundance estimation and differential abundance assessment of individual taxa in metagenomics samples.
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2023-06-16 |
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banner
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public |
BANNER is a tool that lives inside HULK and aims to make sense of hulk histosketches.
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2023-06-16 |
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python-consensuscore2
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public |
PacBio Arrow Consensus library for Sequel data
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2023-06-16 |
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cnvetti
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public |
CNVetti is a CNV caller from HTS data.
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2023-06-16 |
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tagger
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public |
tagger allows you to tag a corpus of documents with search terms that you provide. It is often used to find mentions of proteins, species, diseases, tissues, chemicals and drugs, GO terms, and so forth, in articles in the Medline corpus.
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2023-06-16 |
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perl-bio-tools-phylo-paml
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public |
Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
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2023-06-16 |
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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 |
