https://github.com/snikumbh/seqarchr

seqArchR: Identifying (promoter) sequence architectures de novo using NMF
https://github.com/snikumbh/seqarchr

clustering nmf nonnegative-matrix-factorization promoter-sequence-architectures r r-package scikit-learn sequence-analysis sequence-architectures unsupervised-machine-learning

Last synced: 26 days ago
JSON representation

seqArchR: Identifying (promoter) sequence architectures de novo using NMF

• Host: GitHub
• URL: https://github.com/snikumbh/seqarchr
• Owner: snikumbh
• License: gpl-3.0
• Created: 2021-12-02T00:59:07.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-03-06T20:18:41.000Z (8 months ago)
• Last Synced: 2024-08-10T04:18:36.575Z (3 months ago)
• Topics: clustering, nmf, nonnegative-matrix-factorization, promoter-sequence-architectures, r, r-package, scikit-learn, sequence-analysis, sequence-architectures, unsupervised-machine-learning
• Language: R
• Homepage: https://snikumbh.github.io/seqArchR
• Size: 11.7 MB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        


# seqArchR

[![DOI](https://zenodo.org/badge/188449833.svg)](https://zenodo.org/badge/latestdoi/188449833)

[![codecov](https://codecov.io/gh/snikumbh/seqArchR/branch/main/graph/badge.svg?token=NEjCGuOUlW)](https://codecov.io/gh/snikumbh/seqArchR)

  [![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/seqArchR.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/seqArchR)

  [![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/seqArchR.svg)](http://bioconductor.org/packages/stats/bioc/seqArchR/)

  [![Bioc support](https://bioconductor.org/shields/posts/seqArchR.svg)](https://support.bioconductor.org/tag/seqArchR)

  [![Bioc history](https://bioconductor.org/shields/years-in-bioc/seqArchR.svg)](https://bioconductor.org/packages/release/bioc/html/seqArchR.html#since)

  [![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/seqArchR.svg)](https://bioconductor.org/packages/release/bioc/html/seqArchR.html#since)

  

  

seqArchR is an unsupervised, non-negative matrix factorization (NMF)-based algorithm for discovery of sequence architectures de novo.

Below is a schematic of seqArchR's algorithm.



## Installation

### Python scikit-learn dependency

This package requires the Python module scikit-learn. Please see installation instructions [here](https://scikit-learn.org/stable/install.html).

### To install this package, use 

```r

if (!requireNamespace("remotes", quietly = TRUE)) {

    install.packages("remotes")   

}

remotes::install_github("snikumbh/seqArchR", build_vignettes = FALSE)

``` 

### Usage

```r

# load package

library(seqArchR)

library(Biostrings)

# Creation of one-hot encoded data matrix from FASTA file

# You can use your own FASTA file instead

inputFastaFilename <- system.file("extdata", "example_data.fa", 

                                  package = "seqArchR", 

                                  mustWork = TRUE)

# Specifying dinuc generates dinucleotide features

inputSeqsMat <- seqArchR::prepare_data_from_FASTA(inputFastaFilename,

                                                  sinuc_or_dinuc = "dinuc")

inputSeqsRaw <- seqArchR::prepare_data_from_FASTA(inputFastaFilename, 

                                               raw_seq = TRUE)

nSeqs <- length(inputSeqsRaw)

positions <- seq(1, Biostrings::width(inputSeqsRaw[1]))

# Set seqArchR configuration

# Most arguments have default values

seqArchRconfig <- seqArchR::set_config(

        parallelize = TRUE,

        n_cores = 2,

        n_runs = 100,

        k_min = 1,

        k_max = 20,

        mod_sel_type = "stability",

        bound = 10^-6,

        chunk_size = 100,

	result_aggl = "ward.D",

	result_dist = "euclid",

        flags = list(debug = FALSE, time = TRUE, verbose = TRUE,

                     plot = FALSE)

        )

#

### Call/Run seqArchR

seqArchRresult <- seqArchR::seqArchR(config = seqArchRconfig,

                               seqs_ohe_mat = inputSeqsMat,

                               seqs_raw = inputSeqsRaw,

                               seqs_pos = positions,

                               total_itr = 2,

			       set_ocollation = c(TRUE, FALSE))

```

# Contact

Comments, suggestions, enquiries/requests are welcome! Feel free to email [email protected] or [create an new issue](https://github.com/snikumbh/seqArchR/issues/new)