https://github.com/smithlabcode/preseqr
An R package for estimating library complexity
https://github.com/smithlabcode/preseqr
capture-recapture library-complexity r r-package sequencing sequencing-coverage sequencing-library
Last synced: 6 months ago
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An R package for estimating library complexity
- Host: GitHub
- URL: https://github.com/smithlabcode/preseqr
- Owner: smithlabcode
- Created: 2014-06-20T22:33:31.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2022-09-04T19:54:39.000Z (over 3 years ago)
- Last Synced: 2025-10-03T22:34:11.159Z (7 months ago)
- Topics: capture-recapture, library-complexity, r, r-package, sequencing, sequencing-coverage, sequencing-library
- Language: R
- Homepage:
- Size: 1.55 MB
- Stars: 13
- Watchers: 7
- Forks: 4
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
preseqR
=======
Code in this repository aims to expand the functionality of Preseq and
make it available in the R statistical computing enviroment. There are
five ways this is supposed to work:
1. The basic functionality of the `preseq` program, initially
focusing only on library complexity, is available. These functions
contain the string "rfa" as part of their names.
2. The mathematical routines for doing rational function
approximation via continued fractions were implemented as a
wrapper for existing functionality in C++. This changed since
version 3.1.1, and now all functionality is in R.
3. Fitting a zero-truncated negative binomial distribution to the
sample is available. These functions include the string "ztnb" as
part of the names.
4. The simulation module is used to generate samples based on mixture
of Poisson.
5. Extra functions are provided to estimate the number of species
represented at least r times in a random sample.
See the [preseqR](https://cran.r-project.org/package=preseqR) package
on CRAN for details
UPDATE HISTORY
==============
Updates in version 4.0.0
------------------------
1. Improve the user interface for core functions
2. Add functions to optimize the depth of single-cell whole-genome
sequencing experiments and whole-exome sequencing experiments
3. Add functions to predict the sample coverage, which is the
probability of sampling an observed species from a population
4. Add functions to predict the fraction of k-mers represented at
least r times in a sequencing experiment
Updates in version 3.1.2
------------------------
1. Fixed a bug for removing defects
Updates in version 3.1.1
------------------------
1. Substituted embedded C++ code with R code
2. Removed the dependencies on the software preseq
Updates in version 3.0.1
------------------------
1. Fixed a bug in Chao's estimator
2. Fixed issues for a Solaris C++ compiler.
Updates in version 3.0.0
------------------------
1. We have changed the return types of many functions in the
package. These functions no longer generate estimated accumulative
curves. Instead, they return function types, which are estimators
for the number of species represented by at least r indivdiduals in
a random sample.
2. We added several estimators for predicting the number of species
represented by at least r individuals in a random sample
Updates in version 2.1.1
========================
We have changed the interfaces for most of our exported functions. We
add new estimators for the number of species represented by at least r
individuals in a random sample.
INSTALLATION
============
1. We recommand everyone to install the package `preseqR` from CRAN.
It can be easily done by in an R session by typing:
```R
>install.packages("preseqR")
```
2. The following instructions are for installing the package from the
source. Assume the source code of `preseqR` has been pulled from the
git repo and it is under the current directory. Start a session in an
R interpreter and type:
```R
>install.packages("polynom")
>install.packages("preseqR", repos=NULL, type="source")
```
Note that the package `polynom` is required by `preseqR`.
CONTACTS AND BUG REPORTS
========================
Andrew D. Smith
andrewds@usc.edu
COPYRIGHT AND LICENSE INFORMATION
=================================
Copyright (C) 2017-2022 Chao Deng and Andrew D. Smith
Authors: Chao Deng and Andrew D. Smith
This is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your
option) any later version.
This software is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.