Showing 13 of total 13 results (show query)
bioc
ChemmineR:Cheminformatics Toolkit for R
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
15 stars 10.45 score 253 scripts 12 dependentsbioc
signatureSearch:Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods.
Maintained by Brendan Gongol. Last updated 5 months ago.
softwaregeneexpressiongokeggnetworkenrichmentsequencingcoveragedifferentialexpressioncpp
17 stars 7.18 score 74 scripts 1 dependentsbioc
VennDetail:A package for visualization and extract details
A set of functions to generate high-resolution Venn,Vennpie plot,extract and combine details of these subsets with user datasets in data frame is available.
Maintained by Kai Guo. Last updated 5 months ago.
datarepresentationgraphandnetworkextractvenndiagram
29 stars 6.75 score 65 scriptsbioc
struct:Statistics in R Using Class-based Templates
Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to 'wrap' tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. Ontology lookup has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
5.91 score 76 scripts 3 dependentsbioc
globaltest:Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.
Maintained by Jelle Goeman. Last updated 5 months ago.
microarrayonechannelbioinformaticsdifferentialexpressiongopathways
5.89 score 79 scripts 6 dependents
rjdverse
rjd3toolkit:Utility Functions around 'JDemetra+ 3.0'
R Interface to 'JDemetra+ 3.x' (<https://github.com/jdemetra>) time series analysis software. It provides functions allowing to model time series (create outlier regressors, user-defined calendar regressors, UCARIMA models...), to test the presence of trading days or seasonal effects and also to set specifications in pre-adjustment and benchmarking when using rjd3x13 or rjd3tramoseats.
Maintained by Tanguy Barthelemy. Last updated 5 months ago.
javajdemetraseasonal-adjustmenttime-seriestimeseriesopenjdk
6 stars 5.74 score 48 scripts 16 dependentsbioc
sparrow:Take command of set enrichment analyses through a unified interface
Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.
Maintained by Steve Lianoglou. Last updated 13 days ago.
genesetenrichmentpathwaysbioinformaticsgsea
21 stars 5.74 score 13 scriptsbioc
FamAgg:Pedigree Analysis and Familial Aggregation
Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.
Maintained by Johannes Rainer. Last updated 5 months ago.
1 stars 5.26 score 5 scripts
soumyaray
result:Result Type for Safely Handling Operations that can Succeed or Fail
Allows wrapping values in success() and failure() types to capture the result of operations, along with any status codes. Risky expressions can be wrapped in as_result() and functions wrapped in result() to catch errors and assign the relevant result types. Monadic functions can be bound together as pipelines or transaction scripts using then_try(), to gracefully handle errors at any step.
Maintained by Soumya Ray. Last updated 1 years ago.
4 stars 5.14 score 692 scriptsbioc
rsbml:R support for SBML, using libsbml
Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.
Maintained by Michael Lawrence. Last updated 1 months ago.
graphandnetworkpathwaysnetworklibsbmlcpp
4.71 score 19 scripts 1 dependents
r-forge
distrTEst:Estimation and Testing Classes Based on Package 'distr'
Evaluation (S4-)classes based on package distr for evaluating procedures (estimators/tests) at data/simulation in a unified way.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
3.68 score 3 scripts 1 dependents
johnrstevens
SigTree:Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree
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.
Maintained by John R. Stevens. Last updated 7 years ago.
2.30 score 3 scripts
