Showing 47 of total 47 results (show query)
bioc
PING:Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
Maintained by Renan Sauteraud. Last updated 5 months ago.
clusteringstatisticalmethodvisualizationsequencinggsl
60.0 match 4.00 score 7 scripts
ropensci
taxize:Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
Maintained by Zachary Foster. Last updated 12 days ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
4.0 match 274 stars 13.63 score 1.6k scripts 23 dependentsropensci
sofa:Connector to 'CouchDB'
Provides an interface to the 'NoSQL' database 'CouchDB' (<http://couchdb.apache.org>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' databases such as 'Cloudant'. Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.
Maintained by Yaoxiang Li. Last updated 1 months ago.
couchdbdatabasenosqldocumentscloudantcouchdb-client
6.8 match 33 stars 7.51 score 54 scriptsbioc
RedeR:Interactive visualization and manipulation of nested networks
RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.
Maintained by Mauro Castro. Last updated 5 months ago.
guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology
7.3 match 6.65 score 107 scripts 7 dependentsropensci
elastic:General Purpose Interface to 'Elasticsearch'
Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.
Maintained by Scott Chamberlain. Last updated 2 years ago.
databaseelasticsearchhttpapisearchnosqljavajsondocumentsdata-sciencedatabase-wrapperetl
5.3 match 247 stars 8.98 score 151 scripts 1 dependents
bpoconnor
NO.PING.PONG:Incorporating Previous Findings When Evaluating New Data
Functions for revealing what happens when effect size estimates from previous studies are taken into account when evaluating each new dataset in a study sequence. The analyses can be conducted for cumulative meta-analyses and for Bayesian data analyses. The package contains sample data for a wide selection of research topics. Jointly considering previous findings along with new data is more likely to result in correct conclusions than does the traditional practice of not incorporating previous findings, which often results in a back and forth ping-pong of conclusions when evaluating a sequence of studies. O'Connor & Ermacora (2021, <doi:10.1037/cbs0000259>).
Maintained by Brian P. OConnor. Last updated 12 months ago.
46.3 match 1.00 scorebioc
lionessR:Modeling networks for individual samples using LIONESS
LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.
Maintained by Ping-Han Hsieh. Last updated 5 months ago.
networknetworkinferencegeneexpression
8.2 match 22 stars 5.57 score 17 scriptsropensci
ckanr:Client for the Comprehensive Knowledge Archive Network ('CKAN') API
Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.
Maintained by Francisco Alves. Last updated 2 years ago.
databaseopen-datackanapidatadatasetapi-wrapperckan-api
5.2 match 100 stars 8.67 score 448 scripts 4 dependentsbioc
DegNorm:DegNorm: degradation normalization for RNA-seq data
This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.
Maintained by Ji-Ping Wang. Last updated 5 months ago.
rnaseqnormalizationgeneexpressionalignmentcoveragedifferentialexpressionbatcheffectsoftwaresequencingimmunooncologyqualitycontroldataimportopenblascppopenmp
8.5 match 1 stars 5.20 score 3 scriptsbioc
NuPoP:An R package for nucleosome positioning prediction
NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.
Maintained by Ji-Ping Wang. Last updated 5 months ago.
geneticsvisualizationclassificationnucleosomepositioninghiddenmarkovmodelfortran
8.3 match 5.04 score 11 scriptsbioc
RiboDiPA:Differential pattern analysis for Ribo-seq data
This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.
Maintained by Ji-Ping Wang. Last updated 3 months ago.
riboseqgeneexpressiongeneregulationdifferentialexpressionsequencingcoveragealignmentrnaseqimmunooncologyqualitycontroldataimportsoftwarenormalizationcpp
9.4 match 4.30 score 1 scripts
pingyangchen
milr:Multiple-Instance Logistic Regression with LASSO Penalty
The multiple instance data set consists of many independent subjects (called bags) and each subject is composed of several components (called instances). The outcomes of such data set are binary or categorical responses, and, we can only observe the subject-level outcomes. For example, in manufacturing processes, a subject is labeled as "defective" if at least one of its own components is defective, and otherwise, is labeled as "non-defective". The 'milr' package focuses on the predictive model for the multiple instance data set with binary outcomes and performs the maximum likelihood estimation with the Expectation-Maximization algorithm under the framework of logistic regression. Moreover, the LASSO penalty is attached to the likelihood function for simultaneous parameter estimation and variable selection.
Maintained by Ping-Yang Chen. Last updated 4 years ago.
lasso-penaltymachine-learningopenblascpp
8.3 match 10 stars 4.88 score 15 scripts
sckott
httping:'Ping' 'URLs' to Time 'Requests'
A suite of functions to ping 'URLs' and to time 'HTTP' 'requests'. Designed to work with 'httr'.
Maintained by Scott Chamberlain. Last updated 2 years ago.
httphttp-clienthttp-requestshttping
10.6 match 10 stars 3.70 score 2 scriptsbioc
consensusSeekeR:Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.
Maintained by Astrid Deschênes. Last updated 5 months ago.
biologicalquestionchipseqgeneticsmultiplecomparisontranscriptionpeakdetectionsequencingcoveragechip-seq-analysisgenomic-data-analysisnucleosome-positioning
6.4 match 1 stars 5.26 score 5 scripts 1 dependents
dataoneorg
dataone:R Interface to the DataONE REST API
Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.
Maintained by Matthew B. Jones. Last updated 3 years ago.
3.3 match 36 stars 9.93 score 472 scripts 3 dependentsbioc
RCy3:Functions to Access and Control Cytoscape
Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.
Maintained by Alex Pico. Last updated 5 months ago.
visualizationgraphandnetworkthirdpartyclientnetwork
2.3 match 52 stars 13.39 score 628 scripts 15 dependentsbioc
igvR:igvR: integrative genomics viewer
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Maintained by Arkadiusz Gladki. Last updated 5 months ago.
visualizationthirdpartyclientgenomebrowsers
3.3 match 43 stars 8.31 score 118 scripts
jipingw
SPECIES:Statistical Package for Species Richness Estimation
Implementation of various methods in estimation of species richness or diversity in Wang (2011)<doi:10.18637/jss.v040.i09>.
Maintained by Ji-Ping Wang. Last updated 6 months ago.
8.5 match 2.76 score 57 scripts
py-chung
IPLGP:Identification of Parental Lines via Genomic Prediction
Combining genomic prediction with Monte Carlo simulation, three different strategies are implemented to select parental lines for multiple traits in plant breeding. The selection strategies include (i) GEBV-O considers only genomic estimated breeding values (GEBVs) of the candidate individuals; (ii) GD-O considers only genomic diversity (GD) of the candidate individuals; and (iii) GEBV-GD considers both GEBV and GD. The above method can be seen in Chung PY, Liao CT (2020) <doi:10.1371/journal.pone.0243159>. Multi-trait genomic best linear unbiased prediction (MT-GBLUP) model is used to simultaneously estimate GEBVs of the target traits, and then a selection index is adopted to evaluate the composite performance of an individual.
Maintained by Ping-Yuan Chung. Last updated 7 months ago.
8.4 match 1 stars 2.70 score
jessevent
pingers:Identify, Ping, and Log Internet Provider Connection Data
To assist you with troubleshooting internet connection issues and assist in isolating packet loss on your network. It does this by allowing you to retrieve the top trace route destinations your internet provider uses, and recursively ping each server in series while capturing the results and writing them to a log file. Each iteration it queries the destinations again, before shuffling the sequence of destinations to ensure the analysis is unbiased and consistent across each trace route.
Maintained by Jesse Vent. Last updated 6 years ago.
5.6 match 5 stars 3.40 score 8 scriptsropensci
webchem:Chemical Information from the Web
Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Maintained by Tamás Stirling. Last updated 3 months ago.
cas-numberchemical-informationchemspideridentifierropensciwebscraping
1.8 match 165 stars 10.31 score 173 scripts 10 dependents
mrc-ide
rrq:Simple Redis Queue
Simple Redis queue in R.
Maintained by Rich FitzJohn. Last updated 4 months ago.
2.2 match 24 stars 7.40 score 14 scripts 3 dependents
jbgruber
rollama:Communicate with 'Ollama' to Run Large Language Models Locally
Wraps the 'Ollama' <https://ollama.com> API, which can be used to communicate with generative large language models locally.
Maintained by Johannes B. Gruber. Last updated 1 months ago.
1.8 match 110 stars 8.36 score 52 scripts
doi-usgs
sbtools:USGS ScienceBase Tools
Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
Maintained by David Blodgett. Last updated 10 months ago.
1.9 match 21 stars 7.94 score 127 scripts 2 dependents
sbgraves237
Ecfun:Functions for 'Ecdat'
Functions and vignettes to update data sets in 'Ecdat' and to create, manipulate, plot, and analyze those and similar data sets.
Maintained by Spencer Graves. Last updated 4 months ago.
1.8 match 7.94 score 85 scripts 4 dependents
merck
simtrial:Clinical Trial Simulation
Provides some basic routines for simulating a clinical trial. The primary intent is to provide some tools to generate trial simulations for trials with time to event outcomes. Piecewise exponential failure rates and piecewise constant enrollment rates are the underlying mechanism used to simulate a broad range of scenarios such as those presented in Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>. However, the basic generation of data is done using pipes to allow maximum flexibility for users to meet different needs.
Maintained by Yujie Zhao. Last updated 3 days ago.
1.5 match 21 stars 9.16 score 52 scriptsmerck
gsDesign2:Group Sequential Design with Non-Constant Effect
The goal of 'gsDesign2' is to enable fixed or group sequential design under non-proportional hazards. To enable highly flexible enrollment, time-to-event and time-to-dropout assumptions, 'gsDesign2' offers piecewise constant enrollment, failure rates, and dropout rates for a stratified population. This package includes three methods for designs: average hazard ratio, weighted logrank tests in Yung and Liu (2019) <doi:10.1111/biom.13196>, and MaxCombo tests. Substantial flexibility on top of what is in the 'gsDesign' package is intended for selecting boundaries.
Maintained by Yujie Zhao. Last updated 3 days ago.
1.5 match 22 stars 8.91 score 186 scripts
rucknium
rbch:Extraction and Analysis of Data from the Bitcoin Cash (BCH) Blockchain
Issues RPC-JSON calls to 'bitcoind', the daemon of Bitcoin Cash (BCH), to extract transaction data from the blockchain. BCH is a fork of Bitcoin that permits a greater number of transactions per second. A BCH daemon is available under an MIT license from the Bitcoin Unlimited website <https://www.bitcoinunlimited.info>.
Maintained by Rucknium. Last updated 4 months ago.
5.2 match 3 stars 2.48 score 7 scripts
dleutnant
influxdbr:R Interface to InfluxDB
An R interface to the InfluxDB time series database <https://www.influxdata.com>. This package allows you to fetch and write time series data from/to an InfluxDB server. Additionally, handy wrappers for the Influx Query Language (IQL) to manage and explore a remote database are provided.
Maintained by Dominik Leutnant. Last updated 5 years ago.
databaseinfluxdbtidyversetimeseries
2.0 match 94 stars 5.90 score 28 scripts
theclue
uptimeRobot:Access the UptimeRobot Ping API
Provide a set of wrappers to call all the endpoints of UptimeRobot API which includes various kind of ping, keep-alive and speed tests. See <https://uptimerobot.com/> for more information.
Maintained by Gabriele Baldassarre. Last updated 8 years ago.
3.6 match 2.78 score 12 scripts
statismike
shiny.reglog:Optional Login and Registration Module System for ShinyApps
RegLog system provides a set of shiny modules to handle register procedure for your users, alongside with login, edit credentials and password reset functionality. It provides support for popular SQL databases and optionally googlesheet-based database for easy setup. For email sending it provides support for 'emayili' and 'gmailr' backends. Architecture makes customizing usability pretty straightforward. The authentication system created with shiny.reglog is designed to be optional: user don't need to be logged-in to access your application, but when logged-in the user data can be used to read from and write to relational databases.
Maintained by Michal Kosinski. Last updated 3 years ago.
googlesheetregister-uishiny-applicationssqlite
1.5 match 14 stars 6.45 score 20 scripts
cran
Rlab:Functions and Datasets Required for ST370 Class
Provides functions and datasets required for the ST 370 course at North Carolina State University.
Maintained by Dennis Boos. Last updated 3 years ago.
4.0 match 2.42 score 8 dependentsbioc
QuaternaryProd:Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.
Maintained by Carl Tony Fakhry. Last updated 5 months ago.
graphandnetworkgeneexpressiontranscriptioncpp
1.6 match 4.00 score 1 scripts
hvillalo
echogram:Echogram Visualisation and Analysis
Easily import multi-frequency acoustic data stored in 'HAC' or 'RAW' files (see <http://biblio.uqar.ca/archives/30005500.pdf> for more information on the format), and produce echogram visualisations with predefined or customized color palettes. It is also possible to merge consecutive echograms; mask or delete unwanted echogram areas; model and subtract background noise; and more important, develop, test and interpret different combinations of frequencies in order to perform acoustic filtering of the echogram's data.
Maintained by Héctor Villalobos. Last updated 1 years ago.
1.8 match 3 stars 3.45 score 19 scripts
bpfaff
rbtc:Bitcoin API
Implementation of the RPC-JSON API for Bitcoin and utility functions for address creation and content analysis of the blockchain.
Maintained by Bernhard Pfaff. Last updated 5 months ago.
5.2 match 1.15 score 14 scripts
richelbilderbeek
netmhc2pan:Interface to 'NetMHCIIpan'
The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at <https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/> or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.
1.6 match 1 stars 3.70 score 8 scriptsbpfaff
rneos:XML-RPC Interface to NEOS
Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.
Maintained by Bernhard Pfaff. Last updated 5 years ago.
1.8 match 2.54 score 25 scripts 4 dependents
yuting1214
TensorTest2D:Fitting Second-Order Tensor Data
An implementation of fitting generalized linear models on second-order tensor type data. The functions within this package mainly focus on parameter estimation, including parameter coefficients and standard deviation.
Maintained by Mark Chen. Last updated 8 months ago.
1.6 match 1 stars 2.70 score 5 scriptscran
rfieldclimate:Client for the 'FieldClimate' API
Provides functionality to interact with the 'FieldClimate' API <https://api.fieldclimate.com/v2/docs/>.
Maintained by Eduard Szöcs. Last updated 2 years ago.
2.0 match 1.70 score 1 scripts
schweflo
NLPclient:Stanford 'CoreNLP' Annotation Client
Stanford 'CoreNLP' annotation client. Stanford 'CoreNLP' <https://stanfordnlp.github.io/CoreNLP/index.html> integrates all NLP tools from the Stanford Natural Language Processing Group, including a part-of-speech (POS) tagger, a named entity recognizer (NER), a parser, and a coreference resolution system, and provides model files for the analysis of English. More information can be found in the README.
Maintained by Florian Schwendinger. Last updated 5 years ago.
1.9 match 1.70 score
pedroharaujo
MultipleBubbles:Test and Detection of Explosive Behaviors for Time Series
Provides the Augmented Dickey-Fuller test and its variations to check the existence of bubbles (explosive behavior) for time series, based on the article by Peter C. B. Phillips, Shuping Shi and Jun Yu (2015a) <doi:10.1111/iere.12131>. Some functions may take a while depending on the size of the data used, or the number of Monte Carlo replications applied.
Maintained by Pedro Araujo. Last updated 7 years ago.
1.6 match 5 stars 1.70 score 10 scripts
tspaulding-esa
telemetR:Filter and Analyze Generalised Telemetry Data from Organisms
Analyze telemetry datasets generalized to allow any technology. The filtering steps check for false positives caused by reflected transmissions from surfaces and false pings from other noise generating equipment. The filters are based on JSATS filtering algorithms found in package 'filteRjsats' <https://CRAN.R-project.org/package=filteRjsats> but have been generalized to allow the user to define many of the filtering variables. Additionally, this package contains scripts used to help identify an optimal maximum blanking period as defined in Capello et al (2015) <doi:10.1371/journal.pone.0134002>. The functions were written according to their manuscript description, but have not been reviewed by the authors for accuracy. It is included here as is, without warranty.
Maintained by Taylor Spaulding. Last updated 1 years ago.
0.5 match 2 stars 3.30 score 3 scriptscran
RcppDPR:'Rcpp' Implementation of Dirichlet Process Regression
'Rcpp' reimplementation of the the Bayesian non-parametric Dirichlet Process Regression model for penalized regression first published in Zeng and Zhou (2017) <doi:10.1038/s41467-017-00470-2>. A full Bayesian version is implemented with Gibbs sampling, as well as a faster but less accurate variational Bayes approximation.
Maintained by Mohammad Abu Gazala. Last updated 1 days ago.
1.6 match 1.00 score
dziakj1
VariableScreening:High-Dimensional Screening for Semiparametric Longitudinal Regression
Implements variable screening techniques for ultra-high dimensional regression settings. Techniques for independent (iid) data, varying-coefficient models, and longitudinal data are implemented. The package currently contains three screen functions: screenIID(), screenLD() and screenVCM(), and six methods for simulating dataset: simulateDCSIS(), simulateLD, simulateMVSIS(), simulateMVSISNY(), simulateSIRS() and simulateVCM(). The package is based on the work of Li-Ping ZHU, Lexin LI, Runze LI, and Li-Xing ZHU (2011) <DOI:10.1198/jasa.2011.tm10563>, Runze LI, Wei ZHONG, & Liping ZHU (2012) <DOI:10.1080/01621459.2012.695654>, Jingyuan LIU, Runze LI, & Rongling WU (2014) <DOI:10.1080/01621459.2013.850086> Hengjian CUI, Runze LI, & Wei ZHONG (2015) <DOI:10.1080/01621459.2014.920256>, and Wanghuan CHU, Runze LI and Matthew REIMHERR (2016) <DOI:10.1214/16-AOAS912>.
Maintained by John Dziak. Last updated 3 years ago.
0.5 match 1 stars 1.98 score 16 scripts 2 dependents