bioconda / packages

Package Name Access Summary Updated
perl-cpan-meta public the distribution metadata for a CPAN dist 2018-12-18
perl-exporter-tiny public Exporter with the features of Sub::Exporter but only core dependencies 2018-12-18
perl-test-simple public Basic utilities for writing tests. 2018-12-18
perl-module-corelist public what modules shipped with versions of perl 2018-12-18
perl-archive-zip public Provide an interface to ZIP archive files. 2018-12-18
python-intervaltree public Faster than intervaltree_bio 2018-12-18
perl-text-parsewords public parse text into an array of tokens or array of arrays 2018-12-18
perl-math-bigint public Arbitrary size floating point math package 2018-12-18
perl-parallel-loops public Execute loops using parallel forked subprocesses 2018-12-18
perl-io-socket-ssl public Nearly transparent SSL encapsulation for IO::Socket::INET. 2018-12-18
snp-pileup public Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets 2018-12-18
sevenbridges-python public SBG API python client bindings 2018-12-18
prokka public A tool for the rapid annotation of prokaryotic genomes 2018-12-18
gatk4 public Genome Analysis Toolkit (GATK4) 2018-12-18
picard public Java tools for working with NGS data in the BAM format 2018-12-18
flashlfq public ultrafast label-free quantification algorithm for mass-spectrometry proteomics 2018-12-18
abeona public A simple transcriptome assembler based on kallisto and Cortex graphs. 2018-12-17
bioblend public CloudMan and Galaxy API library 2018-12-17
perl-parallel-forkmanager public A simple parallel processing fork manager 2018-12-17
perl-data-dumper public seeds germane, yet not germinated 2018-12-17
perl-math-derivative public Numeric 1st and 2nd order differentiation. 2018-12-17
bioconductor-biomvcclass public Creates classes used in model-view-controller (MVC) design 2018-12-17
bioconductor-rontotools public Suite of tools for functional analysis. 2018-12-17
bioconductor-paircompviz public This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups. 2018-12-17
bioconductor-oncosimulr public Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them. 2018-12-17
bioconductor-lpnet public lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used. 2018-12-17
bioconductor-nem public The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy. 2018-12-17
bioconductor-hyperdraw public Functions for visualizing hypergraphs. 2018-12-17
bioconductor-flowcl public Semantic labelling of flow cytometric cell populations. 2018-12-17
bioconductor-meigor public Global Optimization 2018-12-17
bioconductor-cnorode public ODE add-on to CellNOptR 2018-12-17
bioconductor-cnorfuzzy public This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL). 2018-12-17
bioconductor-cellnoptr public This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network. 2018-12-17
r-samr public No Summary 2018-12-17
r-pma public Performs Penalized Multivariate Analysis 2018-12-17
bioconductor-mzr public mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS. 2018-12-17
r-metama public Combines either p-values or modified effect sizes from different studies to find differentially expressed genes 2018-12-17
bioconductor-rhdf5lib public Provides C and C++ hdf5 libraries. 2018-12-17
r-fmsb 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. 2018-12-17
r-kinship2 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. 2018-12-17
popdel public Fast structural deletion calling on population-scale short read paired-end germline WGS data. 2018-12-17
perl-libwww-perl public The World-Wide Web library for Perl 2018-12-17
perl-html-tidy public (X)HTML validation in a Perl object 2018-12-17
perl-readonly public Facility for creating read-only scalars, arrays, hashes 2018-12-17
perl-html-formatter public Base class for HTML formatters 2018-12-17
perl-extutils-makemaker public Create a module Makefile 2018-12-17
perl-math-utils public Useful mathematical functions not in Perl 2018-12-17
biofluff public Exploratory analysis and visualization of high-throughput sequencing data 2018-12-17
bioconductor-motiv public This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs. 2018-12-17
bioconductor-snplocs.hsapiens.dbsnp144.grch38 public SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. 2018-12-17
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