bioconda / packages

Package Name Access Summary Updated
gffcompare public GffCompare by Geo Pertea 2019-04-16
grid public Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x). 2019-04-08
hicexplorer public Set of programs to process, analyze and visualize Hi-C data 2019-04-05
bowtie2 public Fast and sensitive read alignment 2019-04-01
bioconductor-rhdf5lib public Provides C and C++ hdf5 libraries. 2019-03-24
scanpy-scripts public A set of wrappers for individual components of the scanpy package. Functions in python packages are hard to call when building workflows outside of python, so this package adds a set of simple wrappers with robust argument parsing. 2019-03-22
stringtie public Transcriptome assembly and quantification for RNA-seq 2019-03-16
peakachu public Peak calling tool for CLIP-seq data. 2019-03-13
blasr public No Summary 2019-03-12
genomicconsensus public No Summary 2019-03-11
trnascan-se public tRNA detection in large-scale genome sequence 2019-03-09
mentalist public The MLST pipeline developed by the PathOGiST research group. 2019-03-09
freebayes public Bayesian haplotype-based polymorphism discovery and genotyping 2019-03-03
bioconductor-dexseq public The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. 2019-02-26
treetime public Maximum-Likelihood dating and ancestral inference for phylogenetic trees 2019-02-25
busco public BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. 2019-02-21
arb-bio-devel public ARB 6 Sequence Analysis Suite 2019-02-14
arb-bio public ARB 6 Sequence Analysis Suite 2019-02-14
arb-bio-tools public ARB 6 Sequence Analysis Suite 2019-02-14
libarbdb public ARB 6 Sequence Analysis Suite 2019-02-14
circos public Circos is a software package for visualizing data and information. It visualizes data in a circular layout 2019-02-05
pizzly public Fast fusion detection using kallisto 2019-01-17
perl-gd public Perl interface to the gd2 graphics library 2019-01-10
bioconductor-deseq2 public Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. 2019-01-01
bioconductor-mzr public mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS. 2018-12-18
fastqc public A quality control tool for high throughput sequence data. 2018-12-13
bioconductor-genomicranges 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. 2018-12-12
bioconductor-xvector public Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk). 2018-12-11
bioconductor-genomeinfodb 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. 2018-12-11
bioconductor-iranges 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. 2018-12-11
bioconductor-s4vectors 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). 2018-12-10
bioconductor-genomeinfodbdata public Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package. 2018-12-10
bioconductor-biocgenerics public S4 generic functions needed by many Bioconductor packages. 2018-12-08
snippy public Rapid bacterial SNP calling and core genome alignments 2018-11-27
bracken public Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. 2018-11-05
rmblast public RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. 2018-09-12
trinity public Trinity RNA-Seq de novo transcriptome assembly 2018-09-12
poretools public poretools: a toolkit for working with nanopore sequencing data from Oxford Nanopore 2018-07-15
fastaindex public No Summary 2018-07-11
logol public Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic) 2018-07-10
r-biclust public The main function biclust provides several algorithms to find biclusters in two-dimensional data: Cheng and Church, Spectral, Plaid Model, Xmotifs and Bimax. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions. 2018-04-26
nspdk public No Summary 2018-02-05
r-ggthemes public Some extra themes, geoms, and scales for ggplot2. Provides ggplot2 themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, Fivethirtyeight, The Economist, Stata, Excel, and The Wall Street Journal, among others. Provides geoms for Tufte s box plot and range frame. 2017-09-18
ruamel.yaml public A YAML package for Python. It is a derivative of Kirill Simonov's PyYAML 3.11 which supports YAML1.1 2017-06-07
sed public sed (stream editor) 2017-06-07
tabulate public Pretty-print tabular data 2017-06-07
r-fdrtool public Estimates both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold. 2017-06-04
gawk public GNU awk 2016-12-09
perl-text-soundex public Implementation of the soundex algorithm. 2016-12-01
libmagic public Implementation of the file(1) command 2016-12-01
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