Showing 27 of total 27 results (show query)
bioboot
bio3d:Biological Structure Analysis
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintained by Barry Grant. Last updated 5 months ago.
125.5 match 5 stars 8.49 score 1.4k scripts 10 dependents
discoleo
Rpdb:Read, Write, Visualize and Manipulate PDB Files
Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.
Maintained by Leonard Mada. Last updated 26 days ago.
29.4 match 4.43 score 68 scripts
nvelden
NGLVieweR:Interactive 3D Visualization of Molecular Structures
Provides an 'htmlwidgets' <https://www.htmlwidgets.org/> interface to 'NGL.js' <http://nglviewer.org/ngl/api/>. 'NGLvieweR' can be used to visualize and interact with protein databank ('PDB') and structural files in R and Shiny applications. It includes a set of API functions to manipulate the viewer after creation in Shiny.
Maintained by Niels van der Velden. Last updated 4 months ago.
nglnglviewerpdbprotein-data-bankshinyshiny-applications
12.8 match 47 stars 7.19 score 55 scripts 1 dependents
cran
rPDBapi:A Comprehensive Interface for Accessing the Protein Data Bank
Streamlines the interaction with the 'RCSB' Protein Data Bank ('PDB') <https://www.rcsb.org/>. This interface offers an intuitive and powerful tool for searching and retrieving a diverse range of data types from the 'PDB'. It includes advanced functionalities like BLAST and sequence motif queries. Built upon the existing XML-based API of the 'PDB', it simplifies the creation of custom requests, thereby enhancing usability and flexibility for researchers.
Maintained by Selcuk Korkmaz. Last updated 5 months ago.
36.0 match 2.40 score 2 scripts
stan-dev
posteriordb:R functionality for posteriordb
R functionality of easy handling of the posteriordb posteriors.
Maintained by Mans Magnusson. Last updated 2 years ago.
22.2 match 8 stars 3.37 score 59 scripts
simonliles
protein8k:Perform Analysis and Create Visualizations of Proteins
Read Protein Data Bank (PDB) files, performs its analysis, and presents the result using different visualization types including 3D. The package also has additional capability for handling Virus Report data from the National Center for Biotechnology Information (NCBI) database.
Maintained by Simon Liles. Last updated 4 years ago.
16.0 match 1 stars 4.00 score 4 scripts
swsoyee
r3dmol:Create Interactive 3D Visualizations of Molecular Data
Create rich and fully interactive 3D visualizations of molecular data. Visualizations can be included in Shiny apps and R markdown documents, or viewed from the R console and 'RStudio' Viewer. 'r3dmol' includes an extensive API to manipulate the visualization after creation, and supports getting data out of the visualization into R. Based on the '3dmol.js' and the 'htmlwidgets' R package.
Maintained by Wei Su. Last updated 1 years ago.
3dcomputational-biologycomputational-chemistryhacktoberfesthtmlwidgetsmolecular-graphicsmolecular-modelingproteinprotein-structurevisualization
8.4 match 90 stars 6.35 score 166 scripts 1 dependents
bioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
6.5 match 37 stars 7.81 score 29 scripts
jpquast
protti:Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Maintained by Jan-Philipp Quast. Last updated 5 months ago.
data-analysislip-msmass-spectrometryomicsproteinproteomicssystems-biology
5.2 match 61 stars 8.58 score 83 scripts
theropod1
paleoDiv:Extracting and Visualizing Paleobiodiversity
Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.
Maintained by Darius Nau. Last updated 5 months ago.
11.6 match 2 stars 2.78 score
nanxstats
protr:Generating Various Numerical Representation Schemes for Protein Sequences
Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.
Maintained by Nan Xiao. Last updated 6 months ago.
bioinformaticsfeature-engineeringfeature-extractionmachine-learningpeptidesprotein-sequencessequence-analysis
3.1 match 52 stars 10.02 score 173 scripts 3 dependents
padrinodb
Rpadrino:Interact with the 'PADRINO' IPM Database
'PADRINO' houses textual representations of Integral Projection Models which can be converted from their table format into full kernels to reproduce or extend an already published analysis. 'Rpadrino' is an R interface to this database. For more information on Integral Projection Models, see Easterling et al. (2000) <doi:10.1890/0012-9658(2000)081[0694:SSSAAN]2.0.CO;2>, Merow et al. (2013) <doi:10.1111/2041-210X.12146>, Rees et al. (2014) <doi:10.1111/1365-2656.12178>, and Metcalf et al. (2015) <doi:10.1111/2041-210X.12405>. See Levin et al. (2021) for more information on 'ipmr', the engine that powers model reconstruction <doi:10.1111/2041-210X.13683>.
Maintained by Sam Levin. Last updated 1 years ago.
5.7 match 2 stars 4.78 score 15 scripts
interstellar-consultation-services
covid19dbcand:Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R Format
Provides different datasets parsed from 'Drugbank' <https://www.drugbank.ca/covid-19> database using 'dbparser' package. It is a smaller version from 'dbdataset' package. It contains only information about COVID-19 possible treatment.
Maintained by Mohammed Ali. Last updated 11 months ago.
datasetdbparserdrugbankdrugbank-database
4.0 match 3 stars 4.48 score 6 scripts
ropensci
biomartr:Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Maintained by Hajk-Georg Drost. Last updated 1 months ago.
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
1.5 match 218 stars 11.35 score 129 scripts 3 dependents
jlp-bioinf
RRNA:Secondary Structure Plotting for RNA
Functions for creating and manipulating RNA secondary structure plots.
Maintained by JP Bida. Last updated 11 months ago.
3.3 match 1 stars 4.33 score 47 scripts 1 dependents
tylermorganwall
raymolecule:Parse and Render Molecular Structures in 3D
Downloads and parses 'SDF' (Structural Description Format) and 'PDB' (Protein Database) files for 3D rendering.
Maintained by Tyler Morgan-Wall. Last updated 1 years ago.
2.5 match 40 stars 4.30 score 7 scriptsbioc
made4:Multivariate analysis of microarray data using ADE4
Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4.
Maintained by Aedin Culhane. Last updated 5 months ago.
clusteringclassificationdimensionreductionprincipalcomponenttranscriptomicsmultiplecomparisongeneexpressionsequencingmicroarray
1.6 match 6.11 score 107 scripts 2 dependentsbioc
rfaRm:An R interface to the Rfam database
rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.
Maintained by Lara Selles Vidal. Last updated 5 months ago.
functionalgenomicsdataimportthirdpartyclientvisualizationmultiplesequencealignment
2.8 match 3.30 score 1 scriptscran
bios2mds:From Biological Sequences to Multidimensional Scaling
Utilities dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results.
Maintained by Marie Chabbert. Last updated 5 years ago.
4.0 match 1 stars 1.90 score
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.
1.2 match 2 stars 5.62 score 23 scripts
mottastefano
SOMMD:Self Organising Maps for the Analysis of Molecular Dynamics Data
Processes data from Molecular Dynamics simulations using Self Organising Maps. Features include the ability to read different input formats. Trajectories can be analysed to identify groups of important frames. Output visualisation can be generated for maps and pathways. Methodological details can be found in Motta S et al (2022) <doi:10.1021/acs.jctc.1c01163>. I/O functions for xtc format files were implemented using the 'xdrfile' library available under open source license. The relevant information can be found in inst/COPYRIGHT.
Maintained by Stefano Motta. Last updated 6 months ago.
3.9 match 1.70 score 4 scripts
lefeup
BoSSA:A Bunch of Structure and Sequence Analysis
Reads and plots phylogenetic placements.
Maintained by Pierre Lefeuvre. Last updated 4 years ago.
1.8 match 3.35 score 15 scriptscran
PdPDB:Pattern Discovery in PDB Structures of Metalloproteins
Looks for amino acid and/or nucleotide patterns and/or small ligands coordinated to a given prosthetic centre. Files have to be in the local file system and contain proper extension.
Maintained by Luca Belmonte. Last updated 7 years ago.
4.8 match 1.00 scorecran
AntibodyForests:Delineating Inter- And Intra-Antibody Repertoire Evolution
The generated wealth of immune repertoire sequencing data requires software to investigate and quantify inter- and intra-antibody repertoire evolution to uncover how B cells evolve during immune responses. Here, we present 'AntibodyForests', a software to investigate and quantify inter- and intra-antibody repertoire evolution.
Maintained by Daphne van Ginneken. Last updated 2 months ago.
1.6 match 2.70 score 2 scriptsropensci
europepmc:R Interface to the Europe PubMed Central RESTful Web Service
An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples.
Maintained by Najko Jahn. Last updated 1 years ago.
bibliometricseurope-pmcpubmedpubmedcentralscientific-literaturescientific-publications
0.5 match 27 stars 7.94 score 122 scripts 2 dependents
wongswk
compas:Conformational Manipulations of Protein Atomic Structures
Manipulate and analyze 3-D structural geometry of Protein Data Bank (PDB) files.
Maintained by Samuel W.K. Wong. Last updated 3 years ago.
0.5 match 1.00 score 6 scripts