Showing 9 of total 9 results (show query)
bioc
dada2:Accurate, high-resolution sample inference from amplicon sequencing data
The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.
Maintained by Benjamin Callahan. Last updated 5 months ago.
immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioconductorbioinformaticsmetabarcodingtaxonomycpp
487 stars 13.17 score 3.0k scripts 4 dependents
lukejharmon
geiger:Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Maintained by Luke Harmon. Last updated 2 years ago.
1 stars 7.84 score 2.3k scripts 28 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 scripts
enricoschumann
PMwR:Portfolio Management with R
Tools for the practical management of financial portfolios: backtesting investment and trading strategies, computing profit/loss and returns, analysing trades, handling lists of transactions, reporting, and more. The package provides a small set of reliable, efficient and convenient tools for processing and analysing trade/portfolio data. The manual provides all the details; it is available from <https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>. Examples and descriptions of new features are provided at <https://enricoschumann.net/notes/PMwR/>.
Maintained by Enrico Schumann. Last updated 16 days ago.
6.13 score 30 scripts
shaunpwilkinson
insect:Informatic Sequence Classification Trees
Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
Maintained by Shaun Wilkinson. Last updated 4 years ago.
14 stars 5.80 score 91 scripts
nalimilan
logmult:Log-Multiplicative Models, Including Association Models
Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe, 1992), a.k.a. log-multiplicative layer effect model (Xie, 1992) <doi:10.2307/2096242>, and several association models: Goodman (1979) <doi:10.2307/2286971> row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi (1990) <doi:10.2307/271086> and by van der Heijden & Mooijaart (1995) <doi:10.1177/0049124195024001002> Functions allow computing the intrinsic association coefficient (see Bouchet-Valat (2022) <doi:10.1177/0049124119852389>) and the Altham (1970) index <doi:10.1111/j.2517-6161.1970.tb00816.x>, including via the Bayes shrinkage estimator proposed by Zhou (2015) <doi:10.1177/0081175015570097>; and the RAS/IPF/Deming-Stephan algorithm.
Maintained by Milan Bouchet-Valat. Last updated 3 years ago.
log-linear-modelmodellingstatistics
4 stars 5.18 score 76 scripts
pdwaggoner
mlbstats:Major League Baseball Player Statistics Calculator
Computational functions for player metrics in major league baseball including batting, pitching, fielding, base-running, and overall player statistics. This package is actively maintained with new metrics being added as they are developed.
Maintained by Philip D. Waggoner. Last updated 6 months ago.
mlbplayer-level-metricssabermetricsstatistics
3.36 score 46 scripts
cran
ips:Interfaces to Phylogenetic Software in R
Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
Maintained by Christoph Heibl. Last updated 11 months ago.
3.18 score 1 dependents
lexizhu
svenssonm:Svensson's Method
Obtain parameters of Svensson's Method, including percentage agreement, systematic change and individual change. Also, the contingency table can be generated. Svensson's Method is a rank-invariant nonparametric method for the analysis of ordered scales which measures the level of change both from systematic and individual aspects. For the details, please refer to Svensson E. Analysis of systematic and random differences between paired ordinal categorical data [dissertation]. Stockholm: Almqvist & Wiksell International; 1993.
Maintained by Yingyan Zhu. Last updated 8 years ago.
2.70 score 6 scripts