Showing 74 of total 74 results (show query)
bioc
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 3 days ago.
visualizationgraphandnetworkthirdpartyclientnetwork
52 stars 13.47 score 628 scripts 17 dependents
cpsievert
LDAvis:Interactive Visualization of Topic Models
Tools to create an interactive web-based visualization of a topic model that has been fit to a corpus of text data using Latent Dirichlet Allocation (LDA). Given the estimated parameters of the topic model, it computes various summary statistics as input to an interactive visualization built with 'D3.js' that is accessed via a browser. The goal is to help users interpret the topics in their 'LDA' topic model.
Maintained by Carson Sievert. Last updated 7 years ago.
javascripttext-miningtopic-modelingvisualization
558 stars 10.93 score 804 scripts 1 dependentsbioc
cBioPortalData:Exposes and Makes Available Data from the cBioPortal Web Resources
The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.
Maintained by Marcel Ramos. Last updated 8 days ago.
softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
33 stars 10.17 score 147 scripts 4 dependentsbioc
RTCGAToolbox:A new tool for exporting TCGA Firehose data
Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.
Maintained by Marcel Ramos. Last updated 3 months ago.
differentialexpressiongeneexpressionsequencing
18 stars 9.75 score 76 scripts 5 dependents
animint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 1 months ago.
64 stars 8.84 score 173 scripts
cefet-rj-dal
harbinger:A Unified Time Series Event Detection Framework
By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Maintained by Eduardo Ogasawara. Last updated 4 months ago.
18 stars 8.32 score 216 scripts
darwin-eu
DrugUtilisation:Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model
Summarise patient-level drug utilisation cohorts using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. New users and prevalent users cohorts can be generated and their characteristics, indication and drug use summarised.
Maintained by Martí Català. Last updated 2 months ago.
8.20 score 156 scripts 2 dependentsbioc
netZooR:Unified methods for the inference and analysis of gene regulatory networks
netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
Maintained by Tara Eicher. Last updated 11 days ago.
networkinferencenetworkgeneregulationgeneexpressiontranscriptionmicroarraygraphandnetworkgene-regulatory-networktranscription-factors
105 stars 7.98 score
ohdsi
CohortGenerator:Cohort Generation for the OMOP Common Data Model
Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Maintained by Anthony Sena. Last updated 6 months ago.
13 stars 7.91 score 165 scriptsohdsi
CohortSymmetry:Sequence Symmetry Analysis Using the Observational Medical Outcomes Partnership Common Data Model
Calculating crude sequence ratio, adjusted sequence ratio and confidence intervals using data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Maintained by Xihang Chen. Last updated 5 days ago.
1 stars 7.52 score 73 scripts
matrix-profile-foundation
tsmp:Time Series with Matrix Profile
A toolkit implementing the Matrix Profile concept that was created by CS-UCR <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Maintained by Francisco Bischoff. Last updated 3 years ago.
algorithmmatrix-profilemotif-searchtime-seriescpp
72 stars 7.29 score 179 scripts 1 dependentsdarwin-eu
DrugExposureDiagnostics:Diagnostics for OMOP Common Data Model Drug Records
Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Maintained by Ger Inberg. Last updated 16 days ago.
4 stars 7.11 score 41 scriptsbioc
categoryCompare:Meta-analysis of high-throughput experiments using feature annotations
Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Maintained by Robert M. Flight. Last updated 5 months ago.
annotationgomultiplecomparisonpathwaysgeneexpressionbioconductor
6 stars 6.68 score
eagerai
kerastuneR:Interface to 'Keras Tuner'
'Keras Tuner' <https://keras-team.github.io/keras-tuner/> is a hypertuning framework made for humans. It aims at making the life of AI practitioners, hypertuner algorithm creators and model designers as simple as possible by providing them with a clean and easy to use API for hypertuning. 'Keras Tuner' makes moving from a base model to a hypertuned one quick and easy by only requiring you to change a few lines of code.
Maintained by Turgut Abdullayev. Last updated 12 months ago.
hyperparameter-tuninghypertuningkeraskeras-tunertensorflowtrial
34 stars 6.61 score 48 scripts
miracum
DQAstats:Core Functions for Data Quality Assessment
Perform data quality assessment ('DQA') of electronic health records ('EHR'). Publication: Kapsner et al. (2021) <doi:10.1055/s-0041-1733847>.
Maintained by Lorenz A. Kapsner. Last updated 27 days ago.
9 stars 6.55 score 4 scripts 1 dependents
gmbecker
switchr:Installing, Managing, and Switching Between Distinct Sets of Installed Packages
Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a development/production release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.
Maintained by Gabriel Becker. Last updated 2 years ago.
59 stars 6.49 score 52 scripts
mathewchamberlain
SignacX:Cell Type Identification and Discovery from Single Cell Gene Expression Data
An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.
Maintained by Mathew Chamberlain. Last updated 2 years ago.
cellular-phenotypesseuratsingle-cell-rna-seq
24 stars 6.46 score 34 scripts
ropensci
dendroNetwork:Create Networks of Dendrochronological Series using Pairwise Similarity
Creating dendrochronological networks based on the similarity between tree-ring series or chronologies. The package includes various functions to compare tree-ring curves building upon the 'dplR' package. The networks can be used to visualise and understand the relations between tree-ring curves. These networks are also very useful to estimate the provenance of wood as described in Visser (2021) <DOI:10.5334/jcaa.79> or wood-use within a structure/context/site as described in Visser and Vorst (2022) <DOI:10.1163/27723194-bja10014>.
Maintained by Ronald Visser. Last updated 2 months ago.
visualizationgraphandnetworkthirdpartyclientnetworkarchaeologydendrochronologydendroprovenancenetwork-analysistree-rings
7 stars 6.05 score 9 scriptsbioc
MOGAMUN:MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks.
Maintained by Elva-María Novoa-del-Toro. Last updated 5 months ago.
systemsbiologygraphandnetworkdifferentialexpressionbiomedicalinformaticstranscriptomicsclusteringnetwork
12 stars 6.03 score 5 scripts
ivan-rivera
RedditExtractoR:Reddit Data Extraction Toolkit
A collection of tools for extracting structured data from <https://www.reddit.com/>.
Maintained by Ivan Rivera. Last updated 2 years ago.
93 stars 6.02 score 153 scriptsropensci
phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
Maintained by Shixiang Wang. Last updated 8 months ago.
blastngenbankpeer-reviewedphylogeneticssequence-alignment
23 stars 5.86 score 156 scriptsbioc
bioCancer:Interactive Multi-Omics Cancers Data Visualization and Analysis
This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.
Maintained by Karim Mezhoud. Last updated 5 months ago.
guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown
20 stars 5.78 score 7 scripts
selcukorkmaz
PubChemR:Interface to the 'PubChem' Database for Chemical Data Retrieval
Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types. Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Maintained by Selcuk Korkmaz. Last updated 6 months ago.
2 stars 5.62 score 23 scriptsbioc
enrichViewNet:From functional enrichment results to biological networks
This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.
Maintained by Astrid Deschênes. Last updated 5 months ago.
biologicalquestionsoftwarenetworknetworkenrichmentgocystocapefunctional-enrichment
5 stars 5.48 score 6 scripts
cjgb
pxR:PC-Axis with R
Provides a set of functions for reading and writing PC-Axis files, used by different statistical organizations around the globe for data dissemination.
Maintained by Carlos J. Gil Bellosta. Last updated 1 years ago.
37 stars 5.34 score 118 scriptsbioc
fedup:Fisher's Test for Enrichment and Depletion of User-Defined Pathways
An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.
Maintained by Catherine Ross. Last updated 5 months ago.
genesetenrichmentpathwaysnetworkenrichmentnetworkbioconductorenrichment
7 stars 5.32 score 10 scripts
paulrougieux
FAOSTAT:Download Data from the FAOSTAT Database
Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations. A list of functions to download statistics from FAOSTAT (database of the FAO <https://www.fao.org/faostat/>) and WDI (database of the World Bank <https://data.worldbank.org/>), and to perform some harmonization operations.
Maintained by Paul Rougieux. Last updated 7 months ago.
5.30 score 132 scriptsbioc
regutools:regutools: an R package for data extraction from RegulonDB
RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.
Maintained by Joselyn Chavez. Last updated 4 months ago.
generegulationgeneexpressionsystemsbiologynetworknetworkinferencevisualizationtranscriptionbioconductorcdsbregulondb
4 stars 5.20 score 6 scriptsbioc
canceR:A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Maintained by Karim Mezhoud. Last updated 5 months ago.
guigeneexpressionclusteringgogenesetenrichmentkeggmultiplecomparisoncancercancer-datagenegene-expressiongene-methylationgene-mutationgene-setsmethylationmskccmutationstcltk
7 stars 5.08 score 17 scriptsmiracum
DIZutils:Utilities for 'DIZ' R Package Development
Utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 4 months ago.
3 stars 5.03 score 5 scripts 2 dependents
motherhack3r
mitre:Cybersecurity MITRE Standards Data and Digraphs
Extract, transform and load MITRE standards. This package gives you an approach to cybersecurity data sets. All data sets are build on runtime downloading raw data from MITRE public services. MITRE <https://www.mitre.org/> is a government-funded research organization based in Bedford and McLean. Current version includes most used standards as data frames. It also provide a list of nodes and edges with all relationships.
Maintained by Humbert Costas. Last updated 4 years ago.
data-driven-securitymitremitre-shield
19 stars 4.98 score 6 scriptsbioc
MSstatsBioNet:Network Analysis for MS-based Proteomics Experiments
A set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques.
Maintained by Anthony Wu. Last updated 2 months ago.
immunooncologymassspectrometryproteomicssoftwarequalitycontrolnetworkenrichmentnetwork
1 stars 4.85 score 3 scripts
yaoxiangli
cmmr:CEU Mass Mediator RESTful API
CEU (CEU San Pablo University) Mass Mediator is an on-line tool for aiding researchers in performing metabolite annotation. 'cmmr' (CEU Mass Mediator RESTful API) allows for programmatic access in R: batch search, batch advanced search, MS/MS (tandem mass spectrometry) search, etc. For more information about the API Endpoint please go to <https://github.com/YaoxiangLi/cmmr>.
Maintained by Yaoxiang Li. Last updated 6 months ago.
batch-searchceu-mass-mediatormetablomicsms-search
15 stars 4.73 score 12 scriptsbioc
GNOSIS:Genomics explorer using statistical and survival analysis in R
GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.
Maintained by Lydia King. Last updated 5 months ago.
5 stars 4.70 score 2 scripts
abuchmueller
Twitmo:Twitter Topic Modeling and Visualization for R
Tailored for topic modeling with tweets and fit for visualization tasks in R. Collect, pre-process and analyze the contents of tweets using LDA and structural topic models (STM). Comes with visualizing capabilities like tweet and hashtag maps and built-in support for 'LDAvis'.
Maintained by Andreas Buchmueller. Last updated 3 years ago.
ctmgeospatialldanlpstmtopic-modelingtwittertwitter-api
20 stars 4.69 score 49 scriptsohdsi
CirceR:Construct Cohort Inclusion and Restriction Criteria Expressions
Wraps the 'CIRCE' (<https://github.com/ohdsi/circe-be>) 'Java' library allowing cohort definition expressions to be edited and converted to 'Markdown' or 'SQL'.
Maintained by Chris Knoll. Last updated 11 months ago.
6 stars 4.58 score 64 scripts
ermlab
LightningR:Tools for Communication with Lightning-Viz Server
The purpose of this package is to enable usage of lightningviz server to be accessible from R. The server itself can be found at http://lightning-viz.org/ and is required to work with this package. Package by itself cannot and will not create any visualizations.
Maintained by Kolodziejski Kamil. Last updated 9 years ago.
32 stars 4.51 score 7 scripts
wactbprot
R4CouchDB:A R Convenience Layer for CouchDB 2.0
Provides a collection of functions for basic database and document management operations such as add (cdbAddDoc()), get (cdbGetDoc()), list access (cdbGetList()) or delete (cdbDeleteDoc()). Every cdbFunction() gets and returns a list() containing the connection setup. Such a list (named 'cdb' in the documentation) can be generated by cdb <- cdbIni(). Moreover, cdb provides some functions respectively functionality e.g cdb$baseUrl() or cdb$getDocRev().
Maintained by Thomas Bock. Last updated 8 years ago.
31 stars 4.45 score 18 scriptsbioc
Macarron:Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
Macarron is a workflow for the prioritization of potentially bioactive metabolites from metabolomics experiments. Prioritization integrates strengths of evidences of bioactivity such as covariation with a known metabolite, abundance relative to a known metabolite and association with an environmental or phenotypic indicator of bioactivity. Broadly, the workflow consists of stratified clustering of metabolic spectral features which co-vary in abundance in a condition, transfer of functional annotations, estimation of relative abundance and differential abundance analysis to identify associations between features and phenotype/condition.
Maintained by Sagun Maharjan. Last updated 5 months ago.
sequencingmetabolomicscoveragefunctionalpredictionclustering
4.41 score 13 scriptsbioc
DEGraph:Two-sample tests on a graph
DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.
Maintained by Laurent Jacob. Last updated 5 months ago.
microarraydifferentialexpressiongraphandnetworknetworknetworkenrichmentdecisiontree
4.34 score 11 scripts
loosolab
wilson:Web-Based Interactive Omics Visualization
Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Maintained by Hendrik Schultheis. Last updated 4 years ago.
2 stars 4.30 score 7 scriptsbioc
CeTF:Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network and can be applied to any correlation-based network including but not limited to gene co-expression networks, while the RIF algorithm identify critical Transcription Factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data).
Maintained by Carlos Alberto Oliveira de Biagi Junior. Last updated 5 months ago.
sequencingrnaseqmicroarraygeneexpressiontranscriptionnormalizationdifferentialexpressionsinglecellnetworkregressionchipseqimmunooncologycoveragecpp
4.30 score 9 scriptsbioc
NCIgraph:Pathways from the NCI Pathways Database
Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.
Maintained by Laurent Jacob. Last updated 5 months ago.
4.26 score 10 scripts 1 dependents
fabsig
gpboost:Combining Tree-Boosting with Gaussian Process and Mixed Effects Models
An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Maintained by Fabio Sigrist. Last updated 1 months ago.
4.17 score 212 scriptsmiracum
DQAgui:Graphical User Interface for Data Quality Assessment
A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. Publication: Mang et al. (2021) <doi:10.1186/s12911-022-01961-z>.
Maintained by Lorenz A. Kapsner. Last updated 2 months ago.
2 stars 4.15 score 10 scripts
kiangkiangkiang
ggESDA:Exploratory Symbolic Data Analysis with 'ggplot2'
Implements an extension of 'ggplot2' and visualizes the symbolic data with multiple plot which can be adjusted by more general and flexible input arguments. It also provides a function to transform the classical data to symbolic data by both clustering algorithm and customized method.
Maintained by Bo-Syue Jiang. Last updated 2 years ago.
21 stars 4.02 score 9 scriptsbioc
transomics2cytoscape:A tool set for 3D Trans-Omic network visualization with Cytoscape
transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).
Maintained by Kozo Nishida. Last updated 5 months ago.
networksoftwarepathwaysdataimportkegg
4.00 score 2 scripts
biologicalrecordscentre
rYoutheria:Access to the YouTheria Mammal Trait Database
A programmatic interface to web-services of YouTheria. YouTheria is an online database of mammalian trait data <http://www.utheria.org.uk/>.
Maintained by Tom August. Last updated 6 years ago.
2 stars 4.00 score 10 scriptsbioc
GladiaTOX:R Package for Processing High Content Screening data
GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.
Maintained by PMP S.A. R Support. Last updated 5 months ago.
softwareworkflowstepnormalizationpreprocessingqualitycontrol
4.00 score 2 scriptsbioc
MetaPhOR:Metabolic Pathway Analysis of RNA
MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.
Maintained by Emily Isenhart. Last updated 5 months ago.
metabolomicsrnaseqpathwaysgeneexpressiondifferentialexpressionkeggsequencingmicroarray
4.00 score 1 scriptsbioc
KEGGlincs:Visualize all edges within a KEGG pathway and overlay LINCS data
See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.
Maintained by Shana White. Last updated 5 months ago.
networkinferencegeneexpressiondatarepresentationthirdpartyclientcellbiologygraphandnetworkpathwayskeggnetwork
4.00 score 3 scripts
onertipaday
RXKCD:Get XKCD Comic from R
Visualize your favorite XKCD comic strip directly from R. XKCD <https://xkcd.com> web comic content is provided under the Creative Commons Attribution-NonCommercial 2.5 License.
Maintained by Paolo Sonego. Last updated 3 years ago.
2 stars 3.79 score 31 scriptsbioc
cbaf:Automated functions for comparing various omic data from cbioportal.org
This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.
Maintained by Arman Shahrisa. Last updated 5 months ago.
softwareassaydomaindnamethylationgeneexpressiontranscriptionmicroarrayresearchfieldbiomedicalinformaticscomparativegenomicsepigeneticsgeneticstranscriptomics
3.78 score 1 scriptsbioc
GeneNetworkBuilder:GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.
Maintained by Jianhong Ou. Last updated 22 days ago.
sequencingmicroarraygraphandnetworkcpp
3.77 score 17 scripts
mikehellstern
netgsa:Network-Based Gene Set Analysis
Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>
Maintained by Michael Hellstern. Last updated 3 years ago.
4 stars 3.75 score 28 scripts
jdthorpe
ajv:Another JSON Schema Validator
A thin wrapper around the 'ajv' JSON validation package for JavaScript. See <http://epoberezkin.github.io/ajv/> for details.
Maintained by Jason Thorpe. Last updated 8 years ago.
3.70 score 8 scripts
aodiakite
casabourse:Casablanca Stock Exchange Data
It provides real-time data from the Casablanca Stock Exchange. The objective is to facilitate access to data for all users of the R programming language. It includes a variety of data accessible just by function call.
Maintained by Abdoul Oudouss Diakité. Last updated 2 years ago.
casablancafinancefinancial-datamoroccostatisticsstock-market
9 stars 3.69 score 11 scripts
ropengov
ogdindiar:API Access to Datasets on Open Government Data - India Portal
Provides API access to selected datasets on Open Government Data - India Portal.
Maintained by Dhrumin Shah. Last updated 2 years ago.
3.60 score 6 scripts
peyronlab
ScriptMapR:R Script Visualization in Cytoscape
Displays the content of a R script into the 'Cytoscape' network-visualization app <https://cytoscape.org/>.
Maintained by Raphaël Bonnet. Last updated 4 years ago.
6 stars 3.48 scorebioc
BaseSpaceR:R SDK for BaseSpace RESTful API
A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.
Maintained by Jared OConnell. Last updated 5 months ago.
infrastructuredatarepresentationconnecttoolssoftwaredataimporthighthroughputsequencingsequencinggenetics
3.30 score 9 scripts
cran
RSDA:R to Symbolic Data Analysis
Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Maintained by Oldemar Rodriguez. Last updated 1 years ago.
1 stars 3.26 score 3 dependentscran
haploR:Query 'HaploReg', 'RegulomeDB'
A set of utilities for querying 'HaploReg' <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>, 'RegulomeDB' <https://www.regulomedb.org/regulome-search/> web-based tools. The package connects to 'HaploReg', 'RegulomeDB' searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.
Maintained by Ilya Y. Zhbannikov. Last updated 1 years ago.
1 stars 3.24 score
chriswweibo
mojson:A Serialization-Style Flattening and Description for JSON
Support JSON flattening in a long data frame way, where the nesting keys will be stored in the absolute path. It also provides an easy way to summarize the basic description of a JSON list. The idea of 'mojson' is to transform a JSON object in an absolute serialization way, which means the early key-value pairs will appear in the heading rows of the resultant data frame. 'mojson' also provides an alternative way of comparing two different JSON lists, returning the left/inner/right-join style results.
Maintained by Bo Wei. Last updated 4 years ago.
1 stars 2.88 score 15 scripts
cbw1243
CropScapeR:Access Cropland Data Layer Data via the 'CropScape' Web Service
Interface to easily access Cropland Data Layer (CDL) data for any area of interest via the 'CropScape' <https://nassgeodata.gmu.edu/CropScape/> web service.
Maintained by Bowen Chen. Last updated 2 years ago.
2.22 score 33 scripts
yevshin
rbiouml:Interact with BioUML Server
Functions for connecting to BioUML server, querying BioUML repository and launching BioUML analyses.
Maintained by Ivan Yevshin. Last updated 4 years ago.
2.18 score 15 scriptscran
pubmed.mineR:Text Mining of PubMed Abstracts
Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Maintained by S. Ramachandran. Last updated 7 months ago.
6 stars 2.08 scorecran
Rgff:R Utilities for GFF Files
R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Maintained by Juan Antonio Garcia-Martin. Last updated 2 years ago.
2.00 score
thospfuller
ropensecretsapi:R Package for the OpenSecrets.org API
An R package for the OpenSecrets.org web services API.
Maintained by Thomas P. Fuller. Last updated 10 years ago.
1.81 score 13 scripts
mingzhuotina
lipidmapsR:Lipid Maps Rest Service
Lipid Maps Rest service. Researchers can access the Lipid Maps Rest service programmatically and conveniently integrate it into the current workflow or packages.
Maintained by Mingzhuo Tian. Last updated 3 years ago.
1.00 scorethospfuller
restimizeapi:Functions for Working with the 'www.estimize.com' Web Services
Provides the user with functions to develop their trading strategy, uncover actionable trading ideas, and monitor consensus shifts with crowdsourced earnings and economic estimate data directly from <www.estimize.com>. Further information regarding the web services this package invokes can be found at <www.estimize.com/api>.
Maintained by Thomas P. Fuller. Last updated 10 years ago.
1.00 score 8 scripts