Showing 18 of total 18 results (show query)
walkerke
tigris:Load Census TIGER/Line Shapefiles
Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as 'sf' objects.
Maintained by Kyle Walker. Last updated 5 months ago.
331 stars 12.87 score 5.3k scripts 16 dependents
bioc
InteractionSet:Base Classes for Storing Genomic Interaction Data
Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.
Maintained by Aaron Lun. Last updated 5 months ago.
infrastructuredatarepresentationsoftwarehiccpp
7.97 score 250 scripts 36 dependents
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scripts
pachadotdev
analogsea:Interface to 'DigitalOcean'
Provides a set of functions for interacting with the 'DigitalOcean' API <https://www.digitalocean.com/>, including creating images, destroying them, rebooting, getting details on regions, and available images.
Maintained by Mauricio Vargas. Last updated 2 years ago.
159 stars 7.54 score 100 scripts 1 dependentsbioc
HiCExperiment:Bioconductor class for interacting with Hi-C files in R
R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.
Maintained by Jacques Serizay. Last updated 10 days ago.
9 stars 7.02 score 48 scripts 2 dependentsbioc
RnBeads:RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Maintained by Fabian Mueller. Last updated 2 months ago.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
6.85 score 169 scripts 1 dependentsbioc
Repitools:Epigenomic tools
Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.
Maintained by Mark Robinson. Last updated 5 months ago.
dnamethylationgeneexpressionmethylseq
5.90 score 267 scripts
statistikat
tatoo:Combine and Export Data Frames
Functions to combine data.frames in ways that require additional effort in base R, and to add metadata (id, title, ...) that can be used for printing and xlsx export. The 'Tatoo_report' class is provided as a convenient helper to write several such tables to a workbook, one table per worksheet. Tatoo is built on top of 'openxlsx', but intimate knowledge of that package is not required to use tatoo.
Maintained by Stefan Fleck. Last updated 2 years ago.
7 stars 5.53 score 24 scripts
usaid-oha-si
mindthegap:Mind the Gap
Package to tidy UNAIDS estimates (from the EDMS database) as well as plot trends in UNAIDS 95 goals and ART coverage gap by country.
Maintained by Karishma Srikanth. Last updated 2 months ago.
5 stars 5.51 score 13 scripts
beanumber
tidychangepoint:A Tidy Framework for Changepoint Detection Analysis
Changepoint detection algorithms for R are widespread but have different interfaces and reporting conventions. This makes the comparative analysis of results difficult. We solve this problem by providing a tidy, unified interface for several different changepoint detection algorithms. We also provide consistent numerical and graphical reporting leveraging the 'broom' and 'ggplot2' packages.
Maintained by Benjamin S. Baumer. Last updated 2 months ago.
2 stars 5.30 score 8 scripts
rkbauer
oceanmap:A Plotting Toolbox for 2D Oceanographic Data
Plotting toolbox for 2D oceanographic data (satellite data, sea surface temperature, chlorophyll, ocean fronts & bathymetry). Recognized classes and formats include netcdf, Raster, '.nc' and '.gz' files.
Maintained by Robert K. Bauer. Last updated 1 years ago.
bathymetrychlaggplotmapping-toolsncdfoceanographic-dataremote-sensingsatellite-imspatial-datasst
4 stars 4.54 score 58 scripts 1 dependents
ropengov
geodk:Access Danish Geospatial Data
This package provides access to all geospatial data provided by the danish agency called Klimadatastyrelsen. Under the hood it wraps the `{dawaR}` and `{dkdata}` packages which provide access to the agency APIs.
Maintained by Aleksander Bang-Larsen. Last updated 17 days ago.
ropengovdenmarkdenmark-mapgeodkgeospatialr-lang
3 stars 4.13 score 15 scriptsbioc
CGHbase:CGHbase: Base functions and classes for arrayCGH data analysis.
Contains functions and classes that are needed by arrayCGH packages.
Maintained by Mark van de Wiel. Last updated 5 months ago.
infrastructuremicroarraycopynumbervariation
3.98 score 3 scripts 8 dependentsbioc
les:Identifying Differential Effects in Tiling Microarray Data
The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.
Maintained by Julian Gehring. Last updated 5 months ago.
microarraydifferentialexpressionchipchipdnamethylationtranscription
3.78 score 3 scripts 1 dependentsbioc
srnadiff:Finding differentially expressed unannotated genomic regions from RNA-seq data
srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.
Maintained by Zytnicki Matthias. Last updated 3 months ago.
immunooncologygeneexpressioncoveragesmallrnaepigeneticsstatisticalmethodpreprocessingdifferentialexpressioncpp
3.70 score 3 scriptsbioc
IWTomics:Interval-Wise Testing for Omics Data
Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.
Maintained by Marzia A Cremona. Last updated 5 months ago.
statisticalmethodmultiplecomparisondifferentialexpressiondifferentialmethylationdifferentialpeakcallinggenomeannotationdataimport
3.30 score 5 scripts
aijordan
triptych:Diagnostic Graphics to Evaluate Forecast Performance
Overall predictive performance is measured by a mean score (or loss), which decomposes into miscalibration, discrimination, and uncertainty components. The main focus is visualization of these distinct and complementary aspects in joint displays. See Dimitriadis, Gneiting, Jordan, Vogel (2024) <doi:10.1016/j.ijforecast.2023.09.007>.
Maintained by Alexander I. Jordan. Last updated 10 months ago.
3.28 score 19 scripts
amineandam04
geomaroc:Easily Visualize Geographic Data of Morocco
Tools to easily visualize geographic data of Morocco. This package interacts with data available through the 'geomarocdata' package, which is available in a 'drat' repository. The size of the 'geomarocdata' package is approximately 12 MB.
Maintained by Amine Andam. Last updated 3 years ago.
2.00 score 4 scripts