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ncftp
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public |
No Summary
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2025-03-25 |
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virulign
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public |
VIRULIGN is a tool for codon-correct pairwise alignments
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2025-03-25 |
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r-motifbinner
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public |
This is an R package for interfacing with the BIOM format.
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2025-03-25 |
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telescope
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public |
Single locus resolution of Transposable ELEment expression.
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2025-03-25 |
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abayesqr
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public |
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.
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2025-03-25 |
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bioconductor-genomeinfodbdata
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public |
Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.
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2025-03-25 |
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bioconductor-genomeinfodb
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public |
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.
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2025-03-25 |
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bioconductor-genomicranges
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public |
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.
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2025-03-25 |
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bioconductor-rsamtools
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public |
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.
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2025-03-25 |
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bioconductor-biobase
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public |
Functions that are needed by many other packages or which replace R functions.
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2025-03-25 |
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bioconductor-biocgenerics
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public |
S4 generic functions needed by many Bioconductor packages.
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2025-03-25 |
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bioconductor-delayedarray
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public |
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.
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2025-03-25 |
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bioconductor-summarizedexperiment
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public |
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.
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2025-03-25 |
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bioconductor-s4vectors
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public |
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).
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2025-03-25 |
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bioconductor-iranges
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public |
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.
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2025-03-25 |
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bioconductor-xvector
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public |
Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).
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2025-03-25 |
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bioconductor-genomicalignments
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public |
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.
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2025-03-25 |
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bioconductor-biocparallel
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public |
This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.
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2025-03-25 |
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bioconductor-zlibbioc
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public |
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.
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2025-03-25 |
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bioconductor-biostrings
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public |
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
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2025-03-25 |
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r-regresshaplo
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public |
A haplotyper in R.
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2025-03-25 |
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r-rmutil
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public |
A toolkit of functions for nonlinear regression and repeated measurements not to be used by itself but called by other Lindsey packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event' (available at <http://www.commanster.eu/rcode.html>).
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2025-03-25 |
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shorah
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public |
The Short Reads Assembly into Haplotypes (ShoRAH) program for inferring viral haplotypes from NGS data
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2025-03-25 |
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transit
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public |
TRANSIT
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2025-03-25 |
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tabix
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public |
A set of tools written in Perl and C++ for working with VCF files.
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2025-03-25 |
