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bioc

Biostrings:Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Maintained by Hervé Pagès. Last updated 1 months ago.

sequencematching alignment sequencing genetics dataimport datarepresentation infrastructure bioconductor-package core-package

62 stars 17.77 score 8.6k scripts 1.2k dependents

bioc

ShortRead:FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

dataimport sequencing qualitycontrol bioconductor-package core-package zlib cpp

8 stars 12.08 score 1.8k scripts 49 dependents

kwstat

pals:Color Palettes, Colormaps, and Tools to Evaluate Them

A comprehensive collection of color palettes, colormaps, and tools to evaluate them. See Kovesi (2015) <doi:10.48550/arXiv.1509.03700>.

Maintained by Kevin Wright. Last updated 23 days ago.

83 stars 11.39 score 2.1k scripts 8 dependents

helske

seqHMM:Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series

Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation. Documentation is available via several vignettes in this page, and the paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).

Maintained by Jouni Helske. Last updated 2 years ago.

categorical-data em-algorithm hidden-markov-models hmm mixture-markov-models time-series openblas cpp openmp

98 stars 8.52 score 92 scripts 1 dependents

traminer

TraMineR:Trajectory Miner: a Sequence Analysis Toolkit

Set of sequence analysis tools for manipulating, describing and rendering categorical sequences, and more generally mining sequence data in the field of social sciences. Although this sequence analysis package is primarily intended for state or event sequences that describe time use or life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent event subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.

Maintained by Gilbert Ritschard. Last updated 4 months ago.

cpp

11 stars 8.24 score 534 scripts 13 dependents

biogenies

tidysq:Tidy Processing and Analysis of Biological Sequences

A tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.

Maintained by Dominik Rafacz. Last updated 3 months ago.

bioconductor bioinformatics biological-sequences fasta s3 sequences tibble tidy tidyverse vctrs cpp

40 stars 7.56 score 38 scripts

bioc

Modstrings:Working with modified nucleotide sequences

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

Maintained by Felix G.M. Ernst. Last updated 5 months ago.

dataimport datarepresentation infrastructure sequencing software bioconductor biostrings dna dna-modifications modified-nucleotides nucleotides rna rna-modification-alphabet rna-modifications sequences

1 stars 6.64 score 5 scripts 8 dependents

bioc

Structstrings:Implementation of the dot bracket annotations with Biostrings

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

Maintained by Felix G.M. Ernst. Last updated 5 months ago.

dataimport datarepresentation infrastructure sequencing software alignment sequencematching bioconductor rna rna-structural-analysis rna-structure sequences structures

4 stars 6.46 score 3 scripts 4 dependents

extendr

b64:Fast and Vectorized Base 64 Engine

Provides a fast, lightweight, and vectorized base 64 engine to encode and decode character and raw vectors as well as files stored on disk. Common base 64 alphabets are supported out of the box including the standard, URL-safe, bcrypt, crypt, 'BinHex', and IMAP-modified UTF-7 alphabets. Custom engines can be created to support unique base 64 encoding and decoding needs.

Maintained by Josiah Parry. Last updated 2 months ago.

rust cargo

16 stars 6.03 score 4 scripts 3 dependents

stla

freewall:A Wrapper of the JavaScript Library 'Freewall'

Creates dynamic grid layouts of images that can be included in 'Shiny' applications and R markdown documents.

Maintained by Stéphane Laurent. Last updated 11 months ago.

javascript

2.70 score 1 scripts

mmaechler

VLMC:Variable Length Markov Chains ('VLMC') Models

Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.

Maintained by Martin Maechler. Last updated 7 months ago.

1.92 score 28 scripts