Package: preseqR 4.0.0

Chao Deng

preseqR: Predicting Species Accumulation Curves

Originally as an R version of Preseq <doi:10.1038/nmeth.2375>, the package has extended its functionality to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When r = 1, the curve is known as the species accumulation curve, or the library complexity curve in high-throughput genomic sequencing. The package includes both parametric and nonparametric methods, as described by Deng C, et al. (2018) <arxiv:1607.02804v3>.

Authors:Chao Deng, Timothy Daley and Andrew D. Smith

preseqR_4.0.0.tar.gz
preseqR_4.0.0.tar.gz(r-4.7-any)preseqR_4.0.0.tar.gz(r-4.6-any)
preseqR_4.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
preseqR/json (API)

# Install 'preseqR' in R:

install.packages('preseqR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Dickens - Dickens' vocabulary
FisherButterfly - Fisher's butterfly data
Shakespeare - Shakespeare's word type frequencies
SRR061157_k31 - K-mer counts of a metagenomic data
SRR1301329_1M_base - Coverage histogram of a WES data
SRR1301329_1M_read - Read counts of a WES data
SRR1301329_base - Coverage histogram of a WES data
SRR1301329_read - Read counts of a WES data
SRR611492 - Coverage histogram of a scWGS data
SRR611492_5M - Coverage histogram of a scWGS data
Twitter - Social network
WillButterfly - Fisher's butterfly data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.89 score 1 stars 1 packages 129 scripts 97 downloads 4 mentions 20 exports 1 dependencies

Last updated from:311a1e5602. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	109
source / vignettes	OK	173
linux-release-x86_64	OK	111
wasm-release	OK	102

Exports:bbc.rSAC cs.rSAC ds.rSAC ds.rSAC.bootstrap fisher.alpha fisher.rSAC kmer.frac.curve kmer.frac.curve.bootstrap preseqR.interpolate.rSAC preseqR.nonreplace.sampling preseqR.optimal.sequencing preseqR.rSAC preseqR.rSAC.bootstrap preseqR.rSAC.sequencing.rmdup preseqR.sample.cov preseqR.sample.cov.bootstrap preseqR.simu.hist preseqR.ztnb.em ztnb.rSAC ztp.rSAC

Dependencies:polynom

Help page	Topics
Predicting r-species accumulation curves	preseqR-package
BBC estimator	bbc.rSAC
CS estimator	cs.rSAC
Dickens' vocabulary	Dickens
RFA estimator	ds.rSAC
RFA estimator with bootstrap	ds.rSAC.bootstrap
Parameter alpha in the logseries estimator	fisher.alpha
Logseries estimator	fisher.rSAC
Fisher's butterfly data	FisherButterfly
Fraction of k-mers observed at least r times	kmer.frac.curve
Fraction of k-mers observed at least r times with bootstrap	kmer.frac.curve.bootstrap
Interpolation	preseqR.interpolate.rSAC
Sampling	preseqR.nonreplace.sampling
Optimal amount of sequencing for scWGS	preseqR.optimal.sequencing
Best practice for r-SAC - a fast version	preseqR.rSAC
Best practice for r-SAC	preseqR.rSAC.bootstrap
Predicting r-SAC in WES/WGS	preseqR.rSAC.sequencing.rmdup
Predicting generalized sample coverage	preseqR.sample.cov
Predicting generalized sample coverage with bootstrap	preseqR.sample.cov.bootstrap
Simulation	preseqR.simu.hist
Fitting a zero-truncated negative binomial distribution	preseqR.ztnb.em
Shakespeare's word type frequencies	Shakespeare
k-mer counts of a metagenomic data	SRR061157_k31
Coverage histogram of a WES data	SRR1301329_1M_base
Read counts of a WES data	SRR1301329_1M_read
Coverage histogram of a WES data	SRR1301329_base
Read counts of a WES data	SRR1301329_read
Coverage histogram of a scWGS data	SRR611492
Coverage histogram of a scWGS data	SRR611492_5M
Social network	Twitter
Fisher's butterfly data	WillButterfly
ZTNB estimator	ztnb.rSAC
ZTP estimator	ztp.rSAC

Package: preseqR 4.0.0

preseqR: Predicting Species Accumulation Curves

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)