Showing 10 of total 10 results (show query)
bioc
plyranges:A fluent interface for manipulating GenomicRanges
A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.
Maintained by Michael Love. Last updated 11 days ago.
infrastructuredatarepresentationworkflowstepcoveragebioconductordata-analysisdplyrgenomic-rangesgenomicstidy-data
144 stars 12.66 score 1.9k scripts 20 dependents
rnabioco
valr:Genome Interval Arithmetic
Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data. Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.
Maintained by Kent Riemondy. Last updated 21 days ago.
bedtoolsgenomeinterval-arithmeticcpp
90 stars 9.69 score 227 scripts
thackl
gggenomes:A Grammar of Graphics for Comparative Genomics
An extension of 'ggplot2' for creating complex genomic maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It implements a layout concept inspired by 'ggraph' and introduces tracks to bring tidiness to the mess that is genomics data.
Maintained by Thomas Hackl. Last updated 2 months ago.
biological-datacomparative-genomicsgenomics-visualizationggplot-extensionggplot2
650 stars 9.56 score 123 scripts
ochoalab
genio:Genetics Input/Output Functions
Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.
Maintained by Alejandro Ochoa. Last updated 1 months ago.
18 stars 8.04 score 213 scripts 4 dependents
bnprks
BPCells:Single Cell Counts Matrices to PCA
> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.
Maintained by Benjamin Parks. Last updated 2 months ago.
184 stars 7.48 score 172 scripts
dwinter
pafr:Read, Manipulate and Visualize 'Pairwise mApping Format' Data
Provides functions to read, process and visualize pairwise sequence alignments in the 'PAF' format used by 'minimap2' and other whole-genome aligners. 'minimap2' is described by Li H. (2018) <doi:10.1093/bioinformatics/bty191>.
Maintained by David Winter. Last updated 4 years ago.
71 stars 6.73 score 75 scripts
nvelden
geneviewer:Gene Cluster Visualizations
Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.
Maintained by Niels van der Velden. Last updated 11 days ago.
70 stars 6.02 score 13 scripts
cran
BGLR:Bayesian Generalized Linear Regression
Bayesian Generalized Linear Regression.
Maintained by Paulino Perez Rodriguez. Last updated 3 days ago.
2 stars 5.31 score 5 dependentsbioc
chipenrich:Gene Set Enrichment For ChIP-seq Peak Data
ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.
Maintained by Kai Wang. Last updated 19 days ago.
immunooncologychipseqepigeneticsfunctionalgenomicsgenesetenrichmenthistonemodificationregression
4.94 score 29 scripts
tyler-hansen
HodgesTools:Common Use Tools for Genomic Analysis
Built by Hodges lab members for current and future Hodges lab members. Other individuals are welcome to use as well. Provides useful functions that the lab uses everyday to analyze various genomic datasets. Critically, only general use functions are provided; functions specific to a given technique are reserved for a separate package. As the lab grows, we expect to continue adding functions to the package to build on previous lab members code.
Maintained by Tyler Hansen. Last updated 2 years ago.
1.70 score 1 scripts