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flowcraft
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public |
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
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2025-03-25 |
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fastq-anonymous
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public |
Change the sequence of a fastq file to enable sharing of confidential information, for troubleshooting of tools.
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2025-03-25 |
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biopet-seqstat
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public |
SeqStat is a package that contains tools to generate stats from a FastQ file, merge those stats for multiple samples, and validate the generated stats files.
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2025-03-25 |
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rdp_classifier
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public |
Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus
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2025-03-25 |
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fasta-splitter
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public |
Divides a large FASTA file into a set of smaller, approximately equally sized files
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2025-03-25 |
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perl-file-util
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public |
Easy, versatile, portable file handling
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2025-03-25 |
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genomestrip
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public |
Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using whole-genome sequencing data
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2025-03-25 |
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r-ngsplotdb-hg38
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public |
HG19 genome database for NGSplot
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2025-03-25 |
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r-ngsplotdb-hg19
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public |
HG19 genome database for NGSplot
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2025-03-25 |
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r-ngsplotdb-mm10
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public |
MM10 genome database for NGSplot
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2025-03-25 |
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ngsplotdb-ngsplotdb-hg19
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public |
HG19 genome database for NGSplot
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2025-03-25 |
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r-ngsplot
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public |
Quick mining and visualization of NGS data by integrating genomic databases
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2025-03-25 |
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biopet-sampleconfig
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public |
#### Tools - ExtractTsv This mean can extract samples, libraries and readgroups from a sample config file.
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2025-03-25 |
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r-lme4qtl
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public |
Linear mixed models (lme4) with flexible covariance structure for qtl and association analysis.
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2025-03-25 |
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r-kinship2
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public |
Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
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2025-03-25 |
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wtdbg
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public |
Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
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2025-03-25 |
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verifybamid2
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public |
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
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2025-03-25 |
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phyluce
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public |
Software for UCE (and general) phylogenomics.
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2025-03-25 |
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confindr
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public |
Detect intra- and inter-species bacterial contamination in NGS reads.
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2025-03-25 |
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bam2fastx
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public |
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
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2025-03-25 |
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pbcopper
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public |
Core C++ library for data structures, algorithms, and utilities
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2025-03-25 |
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pathwaymatcher
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public |
PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome.
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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kipoi
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public |
Kipoi: model zoo for genomics
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2025-03-25 |
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bcov
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public |
BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence.
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2025-03-25 |
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r-taxa
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public |
Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data.
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2025-03-25 |
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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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2025-03-25 |
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meta-sparse
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public |
SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to predict origins of metagenomic reads.
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2025-03-25 |
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ncbi-vdb
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public |
SRA tools database engine.
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2025-03-25 |
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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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2025-03-25 |
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r-sigtree
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public |
Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.
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2025-03-25 |
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r-phyext2
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public |
Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-geiger
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public |
Methods for fitting macroevolutionary models to phylogenetic trees.
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2025-03-25 |
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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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2025-03-25 |
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genomelake
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public |
Simple and efficient random access to genomic data for deep learning models.
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2025-03-25 |
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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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2025-03-25 |
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r-phytools
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public |
Phylogenetic tools for comparative biology
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2025-03-25 |
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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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2025-03-25 |
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splicemap
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public |
Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy.
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2025-03-25 |
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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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2025-03-25 |
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flash2
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public |
Merge paired-end reads from fragments that are shorter than twice the read length
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2025-03-25 |
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r-metalonda
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public |
Identify time intervals of differentially abundant metagenomics features in longitudinal studies.
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2025-03-25 |
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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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2025-03-25 |
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r-annotables
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public |
Provides tables for converting and annotating Ensembl Gene IDs.
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2025-03-25 |
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snpiphy
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public |
An automated snp phylogeny pipeline
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2025-03-25 |
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ctat-mutations
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public |
Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT.
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2025-03-25 |
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r-spieceasi
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public |
Estimate networks from the precision matrix of compositional microbial abundance data.
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2025-03-25 |
