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revolutionanalytics
foreach:Provides Foreach Looping Construct
Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.
Maintained by Folashade Daniel. Last updated 3 years ago.
53 stars 17.21 score 43k scripts 2.8k dependents
bioc
MGnifyR:R interface to EBI MGnify metagenomics resource
Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.
Maintained by Tuomas Borman. Last updated 3 days ago.
infrastructuredataimportmetagenomicsmicrobiomemicrobiomedata
21 stars 7.48 score 32 scripts
surmann
ODEnetwork:Network of Differential Equations
Simulates a network of ordinary differential equations of order two. The package provides an easy interface to construct networks. In addition you are able to define different external triggers to manipulate the trajectory. The method is described by Surmann, Ligges, and Weihs (2014) <doi:10.1109/ENERGYCON.2014.6850482>.
Maintained by Dirk Surmann. Last updated 5 years ago.
4 stars 5.08 score 20 scripts 1 dependentsbioc
TCC:TCC: Differential expression analysis for tag count data with robust normalization strategies
This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.
Maintained by Jianqiang Sun. Last updated 5 months ago.
immunooncologysequencingdifferentialexpressionrnaseq
4.91 score 41 scriptsbioc
HoloFoodR:R interface to EBI HoloFood resource
Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.
Maintained by Tuomas Borman. Last updated 1 months ago.
softwareinfrastructuredataimportmicrobiomemicrobiomedata
1 stars 4.70 score 6 scriptsbioc
MAGAR:MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.
Maintained by Michael Scherer. Last updated 5 months ago.
regressionepigeneticsdnamethylationsnpgeneticvariabilitymethylationarraymicroarraycpgislandmethylseqsequencingmrnamicroarraypreprocessingcopynumbervariationtwochannelimmunooncologydifferentialmethylationbatcheffectqualitycontroldataimportnetworkclusteringgraphandnetwork
4.30 score 3 scripts
gk-crop
simplace:Interface to Use the Modelling Framework 'SIMPLACE'
Interface to interact with the modelling framework 'SIMPLACE' and to parse the results of simulations.
Maintained by Gunther Krauss. Last updated 6 months ago.
1 stars 4.18 score 6 scripts 1 dependents