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perl-cpan-meta
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public |
the distribution metadata for a CPAN dist
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2018-12-18 |
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perl-exporter-tiny
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public |
Exporter with the features of Sub::Exporter but only core dependencies
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2018-12-18 |
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perl-test-simple
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public |
Basic utilities for writing tests.
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2018-12-18 |
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perl-module-corelist
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public |
what modules shipped with versions of perl
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2018-12-18 |
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perl-archive-zip
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public |
Provide an interface to ZIP archive files.
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2018-12-18 |
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python-intervaltree
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public |
Faster than intervaltree_bio
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2018-12-18 |
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perl-text-parsewords
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public |
parse text into an array of tokens or array of arrays
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2018-12-18 |
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perl-math-bigint
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public |
Arbitrary size floating point math package
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2018-12-18 |
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perl-parallel-loops
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public |
Execute loops using parallel forked subprocesses
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2018-12-18 |
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perl-io-socket-ssl
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public |
Nearly transparent SSL encapsulation for IO::Socket::INET.
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2018-12-18 |
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snp-pileup
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public |
Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets
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2018-12-18 |
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sevenbridges-python
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public |
SBG API python client bindings
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2018-12-18 |
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prokka
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public |
A tool for the rapid annotation of prokaryotic genomes
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2018-12-18 |
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gatk4
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public |
Genome Analysis Toolkit (GATK4)
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2018-12-18 |
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picard
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public |
Java tools for working with NGS data in the BAM format
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2018-12-18 |
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flashlfq
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public |
ultrafast label-free quantification algorithm for mass-spectrometry proteomics
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2018-12-18 |
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abeona
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public |
A simple transcriptome assembler based on kallisto and Cortex graphs.
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2018-12-17 |
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bioblend
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public |
CloudMan and Galaxy API library
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2018-12-17 |
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perl-parallel-forkmanager
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public |
A simple parallel processing fork manager
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2018-12-17 |
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perl-data-dumper
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public |
seeds germane, yet not germinated
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2018-12-17 |
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perl-math-derivative
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public |
Numeric 1st and 2nd order differentiation.
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2018-12-17 |
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bioconductor-biomvcclass
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public |
Creates classes used in model-view-controller (MVC) design
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2018-12-17 |
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bioconductor-rontotools
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public |
Suite of tools for functional analysis.
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2018-12-17 |
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bioconductor-paircompviz
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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.
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2018-12-17 |
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bioconductor-oncosimulr
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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.
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2018-12-17 |
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bioconductor-lpnet
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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.
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2018-12-17 |
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bioconductor-nem
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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.
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2018-12-17 |
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bioconductor-hyperdraw
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public |
Functions for visualizing hypergraphs.
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2018-12-17 |
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bioconductor-flowcl
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public |
Semantic labelling of flow cytometric cell populations.
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2018-12-17 |
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bioconductor-meigor
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public |
Global Optimization
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2018-12-17 |
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bioconductor-cnorode
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public |
ODE add-on to CellNOptR
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2018-12-17 |
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bioconductor-cnorfuzzy
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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).
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2018-12-17 |
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bioconductor-cellnoptr
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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.
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2018-12-17 |
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r-samr
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public |
No Summary
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2018-12-17 |
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r-pma
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public |
Performs Penalized Multivariate Analysis
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2018-12-17 |
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bioconductor-mzr
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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.
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2018-12-17 |
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r-metama
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public |
Combines either p-values or modified effect sizes from different studies to find differentially expressed genes
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2018-12-17 |
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bioconductor-rhdf5lib
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public |
Provides C and C++ hdf5 libraries.
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2018-12-17 |
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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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2018-12-17 |
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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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2018-12-17 |
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popdel
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public |
Fast structural deletion calling on population-scale short read paired-end germline WGS data.
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2018-12-17 |
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perl-libwww-perl
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public |
The World-Wide Web library for Perl
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2018-12-17 |
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perl-html-tidy
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public |
(X)HTML validation in a Perl object
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2018-12-17 |
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perl-readonly
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public |
Facility for creating read-only scalars, arrays, hashes
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2018-12-17 |
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perl-html-formatter
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public |
Base class for HTML formatters
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2018-12-17 |
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perl-extutils-makemaker
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public |
Create a module Makefile
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2018-12-17 |
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perl-math-utils
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public |
Useful mathematical functions not in Perl
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2018-12-17 |
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biofluff
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public |
Exploratory analysis and visualization of high-throughput sequencing data
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2018-12-17 |
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bioconductor-motiv
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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.
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2018-12-17 |
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bioconductor-snplocs.hsapiens.dbsnp144.grch38
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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.
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2018-12-17 |