Showing 11 of total 11 results (show query)
rdatatable
data.table:Extension of `data.frame`
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Maintained by Tyson Barrett. Last updated 3 days ago.
3.7k stars 23.51 score 230k scripts 4.6k dependents
bioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
8 stars 12.08 score 1.8k scripts 49 dependents
majkamichal
naivebayes:High Performance Implementation of the Naive Bayes Algorithm
In this implementation of the Naive Bayes classifier following class conditional distributions are available: 'Bernoulli', 'Categorical', 'Gaussian', 'Poisson', 'Multinomial' and non-parametric representation of the class conditional density estimated via Kernel Density Estimation. Implemented classifiers handle missing data and can take advantage of sparse data.
Maintained by Michal Majka. Last updated 2 months ago.
classification-modeldatasciencemachine-learningnaive-bayes
37 stars 10.47 score 1.0k scripts 6 dependents
hope-data-science
tidyfst:Tidy Verbs for Fast Data Manipulation
A toolkit of tidy data manipulation verbs with 'data.table' as the backend. Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table', 'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain. This package is an extension of 'data.table'. While enjoying a tidy syntax, it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Maintained by Tian-Yuan Huang. Last updated 7 months ago.
100 stars 10.06 score 118 scripts 4 dependentsbioc
CompoundDb:Creating and Using (Chemical) Compound Annotation Databases
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
Maintained by Johannes Rainer. Last updated 2 months ago.
massspectrometrymetabolomicsannotationdatabasesmass-spectrometry
17 stars 8.35 score 69 scripts 1 dependentsbioc
musicatk:Mutational Signature Comprehensive Analysis Toolkit
Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.
Maintained by Joshua D. Campbell. Last updated 5 months ago.
softwarebiologicalquestionsomaticmutationvariantannotation
13 stars 6.97 score 20 scriptshope-data-science
tidyft:Fast and Memory Efficient Data Operations in Tidy Syntax
Tidy syntax for 'data.table', using modification by reference whenever possible. This toolkit is designed for big data analysis in high-performance desktop or laptop computers. The syntax of the package is similar or identical to 'tidyverse'. It is user friendly, memory efficient and time saving. For more information, check its ancestor package 'tidyfst'.
Maintained by Tian-Yuan Huang. Last updated 6 months ago.
35 stars 6.25 score 34 scriptsbioc
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
rje42
contingency:Discrete Multivariate Probability Distributions
Provides an object class for dealing with many multivariate probability distributions at once, useful for simulation.
Maintained by Robin Evans. Last updated 7 months ago.
4.00 score 5 scripts
wilsonfreitas
sqliter:Connection wrapper to SQLite databases
sqliter helps users, mainly data munging practioneers, to organize their sql calls in a clean structure. It simplifies the process of extracting and transforming data into useful formats.
Maintained by Wilson Freitas. Last updated 10 years ago.
1 stars 2.70 score 5 scripts
cran
ds:Descriptive Statistics
Performs various analyzes of descriptive statistics, including correlations, graphics and tables.
Maintained by Emmanuel Arnhold. Last updated 6 years ago.
1.70 score