davebx
by davebx
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| Name | Latest Version | Summary | Updated | License |
|---|
| abayesqr | 1.0.0 | aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data. The search for the most likely quasispecies is conducted on long contigs constructed from the set of short reads, which enables identification of closely related haplotypes in a population and provides computational tractability of the Bayesian method. aBayesQR is the first method which is capable of detecting and reliably reconstructing viral haplotypes having very small mutual genetic distances. | Mar 25, 2025 | MIT |
| bioconductor-biobase | 2.42.0 | Functions that are needed by many other packages or which replace R functions. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-biocgenerics | 0.28.0 | S4 generic functions needed by many Bioconductor packages. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-biocparallel | 1.16.5 | This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects. | Mar 25, 2025 | GPL-2 | GPL-3 |
| bioconductor-biostrings | 2.50.2 | Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-delayedarray | 0.8.0 | Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-genomeinfodb | 1.18.1 | Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-genomeinfodbdata | 1.2.0 | Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-genomicalignments | 1.18.1 | Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-genomicranges | 1.34.0 | The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-iranges | 2.16.0 | Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-rsamtools | 1.34.0 | This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files. | Mar 25, 2025 | Artistic-2.0 | file LICENSE |
| bioconductor-s4vectors | 0.20.1 | The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages). | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-summarizedexperiment | 1.12.0 | The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-xvector | 0.22.0 | Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk). | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-zlibbioc | 1.28.0 | This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use. | Mar 25, 2025 | Artistic-2.0 + file LICENSE |
| fastx_toolkit | 0.0.14 | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others. However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks. | Mar 25, 2025 | AGPL |
| gcc | 4.9.4 | The GNU Compiler Collection | Mar 25, 2025 | GPL |
| hicpro | 2.10.0 | An intuitive HyPhy interface for Python | Mar 25, 2025 | GPL-3 |
| hyphy | 2.5.2 | An open-source software package for comparative sequence analysis using stochastic evolutionary models. | Mar 25, 2025 | MIT |
| ncftp | 3.2.6 | — | Mar 25, 2025 | — |
| poreplex | 0.2 | Signal-level preprocessor for Oxford Nanopore direct RNA sequencing (DRS) data. Poreplex does many preprocessing steps required before the downstream analyses for RNA Biology and yields the processed data in the ready-to-use forms. | Mar 25, 2025 | MIT License |
| python-bioext | 0.18.6 | A few handy bioinformatics tools not already in BioPython | Mar 25, 2025 | GPL-3 |
| python-hivclustering | 1.4.0 | A Python 3 library that makes inferences on HIV-1 transmission networks. | Mar 25, 2025 | MIT |
| python-hyphy-python | 0.1.6 | HyPhy package interface library | Mar 25, 2025 | UNKNOWN |