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lorikeet
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public |
Tool for digital spoligotyping of MTB strains from Illumina read data
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2023-06-16 |
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biopet-validatefastq
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public |
This tool validates a FASTQ file.
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2023-06-16 |
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r-pma
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public |
Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in the following papers: (1) Witten, Tibshirani and Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology 8(1): Article 28.
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2023-06-16 |
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r-geiger
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public |
Methods for fitting macroevolutionary models to phylogenetic trees.
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2023-06-16 |
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bax2bam
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public |
bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format
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2023-06-16 |
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itero
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public |
A pipeline for iterative, guided contig assembly that integrates spades, bwa, and samtools to produce assembled contigs.
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2023-06-16 |
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r-funrar
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public |
Computes functional rarity indices as proposed by Violle et al. (2017)
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2023-06-16 |
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logol
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public |
Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic)
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2023-06-16 |
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r-ncbit
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public |
making NCBI taxonomic data locally available and searchable as an R object
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2023-06-16 |
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pisces
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public |
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
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2023-06-16 |
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r-msm
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public |
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. Designed for processes observed at arbitrary times in continuous time (panel data) but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.
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2023-06-16 |
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r-nodiv
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public |
An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
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2023-06-16 |
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biopet-extractadaptersfastqc
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public |
ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report.
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2023-06-16 |
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r-treesim
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public |
Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
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2023-06-16 |
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r-aptreeshape
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public |
Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) and Maliet et al. (2017).
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2023-06-16 |
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snpiphy
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public |
An automated snp phylogeny pipeline
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2023-06-16 |
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iclipro
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public |
iCLIPro is a Python package that can be used to control for systematic misassignments in iCLIP data.
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2023-06-16 |
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dimspy
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public |
Python package for data processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data
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2023-06-16 |
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r-phylobase
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public |
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
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2023-06-16 |
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r-oai
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public |
A general purpose client to work with any 'OAI-PMH' (Open Archives Initiative Protocol for 'Metadata' Harvesting) service. The 'OAI-PMH' protocol is described at <http://www.openarchives.org/OAI/openarchivesprotocol.html>. Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord', 'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and 'ListSets'.
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2023-06-16 |
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r-rbison
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public |
Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>) 'API', a 'database' for species occurrence data. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data.
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2023-06-16 |
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r-ecodist
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public |
Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.
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2023-06-16 |
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r-rvertnet
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public |
Retrieve, map and summarize data from the 'VertNet.org' archives (<http://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
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2023-06-16 |
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r-ridigbio
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public |
An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
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2023-06-16 |
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r-geoaxe
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public |
Split 'geospatial' objects into pieces. Includes support for some spatial object inputs, 'Well-Known Text', and 'GeoJSON'.
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2023-06-16 |
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illumiprocessor
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public |
illumiprocessor is a tool to batch process illumina sequencing reads using the excellent trimmomatic package.
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2023-06-16 |
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r-wicket
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public |
Utilities to generate bounding boxes from 'WKT' (Well-Known Text) objects and R data types, validate 'WKT' objects and convert object types from the 'sp' package into 'WKT' representations.
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2023-06-16 |
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r-adephylo
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public |
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
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2023-06-16 |
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snpsplit
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public |
SNPsplit is an allele-specific alignment sorter which is designed to read in alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.
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2023-06-16 |
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womtool
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public |
Command line utilities for interacting with WDL
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2023-06-16 |
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real
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public |
REad ALigner for Next-Generation sequencing reads.
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2023-06-16 |
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r-propcis
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public |
Computes two-sample confidence intervals for single, paired and independent proportions.
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2023-06-16 |
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bsmap
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public |
BSMAP is a short reads mapping software for bisulfite sequencing reads.
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2023-06-16 |
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ngmerge
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public |
Merging paired-end reads and removing sequencing adapters.
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2023-06-16 |
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cortex_con
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public |
cortex_con (primary contact Mario Caccamo) is for consensus genome assembly
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2023-06-16 |
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esimsa
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public |
Simple deconvolution of electrospray ionization peak lists
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2023-06-16 |
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idr-py
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public |
Helper methods for accessing the Image Data Resource (IDR)
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2023-06-16 |
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spotyping
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public |
SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
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2023-06-16 |
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blobtools
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public |
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
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2023-06-16 |
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cdna_cupcake
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public |
cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
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2023-06-16 |
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riboraptor
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public |
Python package to analyse ribosome profiling data
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2023-06-16 |
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erds
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public |
Inferring copy number variants in high-coverage human genomes with next-generation sequencing data.
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2023-06-16 |
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r-genometricorr
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public |
Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
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2023-06-16 |
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ctat-lncrna
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public |
ctat-lncrna uses slncky
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2023-06-16 |
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r-fmsb
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public |
Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
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2023-06-16 |
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jali
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public |
Alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.
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2023-06-16 |
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biopet-vcfstats
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public |
Vcfstats is a tool that can generate metrics from a vcf file.
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2023-06-16 |
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bibliospec
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public |
The BiblioSpec Spetral Library tool suite
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2023-06-16 |
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perl-extutils-cbuilder
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public |
Compile and link C code for Perl modules
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2023-06-16 |
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mmvc
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public |
Call variants based on a Bayesian multinomial mixture model.
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2023-06-16 |
