Package: seqArchR 1.9.0

Sarvesh Nikumbh

seqArchR: Identify Different Architectures of Sequence Elements

seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

Authors:Sarvesh Nikumbh [aut, cre, cph]

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seqArchR.pdf |seqArchR.html✨
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NEWS

# Install 'seqArchR' in R:

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

Bug tracker:https://github.com/snikumbh/seqarchr/issues

On BioConductor:seqArchR-1.9.0(bioc 3.20)seqArchR-1.8.0(bioc 3.19)

bioconductor-package

18 exports 0.82 score 81 dependencies 1 dependents

Last updated 2 months agofrom:2fbbdc7009

Exports:collate_clusters collate_seqArchR_result get_clBasVec get_clBasVec_k get_clBasVec_m get_one_hot_encoded_seqs get_seqClLab get_seqs_clust_list make_PWMs plot_arch_for_clusters plot_ggseqlogo_of_seqs prepare_data_from_FASTA seqArchR seqs_str set_config viz_bas_vec viz_pwm viz_seqs_acgt_mat

Dependencies:askpass BH BiocGenerics BiocParallel Biostrings class cli cluster codetools colorspace cpp11 crayon curl cvTools DEoptimR diptest fansi farver flexmix formatR fpc futile.logger futile.options GenomeInfoDb GenomeInfoDbData ggplot2 ggseqlogo glue gtable here httr IRanges isoband jsonlite kernlab labeling lambda.r lattice lifecycle magrittr MASS Matrix matrixStats mclust mgcv mime modeltools munsell nlme nnet openssl pillar pkgconfig plyr png prabclus prettyunits R6 rappdirs RColorBrewer Rcpp RcppTOML reshape2 reticulate rlang robustbase rprojroot S4Vectors scales snow stringi stringr sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Example usage of seqArchR on simulated DNA sequences

Sarvesh Nikumbh

Rendered fromseqArchR.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2022-04-01
Started: 2021-12-02

Help page	Topics
Collate sequence IDs from an existing clustering according to a new, given clustering of the existing clusters	collate_clusters
Collate raw clusters at the chosen iteration of seqArchR result	collate_seqArchR_result
Get functions for seqArchR result object	get_clBasVec get_clBasVec_k get_clBasVec_m get_seqClLab
Get one-hot encoded sequences	get_one_hot_encoded_seqs
Retrieve sequence clusters as a list from the sequence labels	get_seqs_clust_list
Make a PWM-resembling matrix out of a given n-vector	make_PWMs
Plot cluster architectures as sequence logos.	plot_arch_for_clusters
Plot sequence logo of a collection of sequences	plot_ggseqlogo_of_seqs
Generate one-hot encoding of sequences given as FASTA file	prepare_data_from_FASTA
seqArchR: A package for de novo discovery of different sequence architectures	seqArchR
Get sequences from the seqArchR result object	seqs_str
Set seqArchR run configuration	set_config
Visualize the NMF basis vectors	viz_bas_vec
Visualize a position weight matrix as a heatmap or sequence logo	viz_pwm
Visualize raw DNA sequences as an image	viz_seqs_acgt_mat

Package: seqArchR 1.9.0

seqArchR: Identify Different Architectures of Sequence Elements

Example usage of seqArchR on simulated DNA sequences

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