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r-corbi
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public |
Provides a bundle of basic and fundamental bioinformatics tools, such as network querying and alignment, subnetwork extraction and search, network biomarker identification.
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2023-06-16 |
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bioexcel_seqqc
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public |
Sequence Quality Control pipeline/modules
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2023-06-16 |
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r-sads
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public |
Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.
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2023-06-16 |
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avro-cwl
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public |
Avro is a serialization and RPC framework. This package is a fork of regular avro made by the CWL team in order to fix some issues (https://github.com/common-workflow-language/cwltool/issues/524)
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2023-06-16 |
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mhcnames
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public |
Python library for MHC nomenclature parsing
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2023-06-16 |
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r-guilds
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public |
A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
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2023-06-16 |
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nimnexus
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public |
command-line tools for processing ChIP-nexus data
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2023-06-16 |
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r-ebimetagenomics
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public |
Functions for querying the EBI Metagenomics Portal <https://www.ebi.ac.uk/metagenomics/>. The current main focus is on taxa abundance data, but the intention is that this package should evolve into a general purpose package for working with EBI Metagenomics data using R.
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2023-06-16 |
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grid
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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).
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2023-06-16 |
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r-mvr
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public |
This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include: (i) Normalization and/or variance stabilization of the data, (ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow), (iii) Generation of diverse diagnostic plots, (iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
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2023-06-16 |
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r-airr
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public |
Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community <http://docs.airr-community.org>.
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2023-06-16 |
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diamond_add_taxonomy
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public |
Utility to work with NCBI taxonomy database including tool to annotate DIAMOND results with taxonomy lineage
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2023-06-16 |
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qcat
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public |
Qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
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2023-06-16 |
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transit
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public |
TRANSIT
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2023-06-16 |
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perl-clone-choose
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public |
Choose appropriate clone utility
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2023-06-16 |
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bioconductor-metavizr
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public |
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
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2023-06-16 |
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cgat-daisy
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public |
A system to design and execute benchmarks
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2023-06-16 |
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biobb_md
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public |
Deprecated Package: biobb_md is no longer maintained and has been superseded by the biobb_gromacs package. Biobb_md is the Biobb module collection to perform molecular dynamics simulations.
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2023-06-16 |
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kipoi
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public |
Kipoi: model zoo for genomics
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2023-06-16 |
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prince
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public |
PRINCE estimates Variable Number Tandem Repeats (VNTR) copy number from raw next generation sequencing (NGS) data.
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2023-06-16 |
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wgfast
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public |
The whole genome focused array SNP typing (WG-FAST) pipeline
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2023-06-16 |
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bioconductor-ippd
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public |
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
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2023-06-16 |
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r-shazam
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public |
Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
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2023-06-16 |
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bioconductor-pathprint
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public |
Pathway fingerprinting for analysis of gene expression arrays
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2023-06-16 |
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bioconductor-chipxpress
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public |
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
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2023-06-16 |
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sbpipe
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public |
SBpipe is a collection of pipelines for systems modelling of biological networks. It allows mathematical modellers to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. SBpipe can run models implemented in COPASI, Python or coded in any other programming language using Python as a wrapper module. Pipelines can run on multicore computers, Sun Grid Engine (SGE), Load Sharing Facility (LSF) clusters, or via Snakemake.
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2023-06-16 |
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fgmp
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public |
FGMP: assessing fungal genome completeness and gene content.
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2023-06-16 |
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gneiss
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public |
Compositional data analysis tools and visualizations
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2023-06-16 |
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bioconductor-rariant
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public |
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
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2023-06-16 |
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sompy
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public |
Numpy based SOM Library.
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2023-06-16 |
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perl-number-range
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public |
Perl extension defining ranges of numbers and testing if a number is found in the range
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2023-06-16 |
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pydemult
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public |
Streamed and parallel demultiplexing of fastq files in python
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2023-06-16 |
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bioconductor-networkbma
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public |
Regression-based network inference using Bayesian Model Averaging
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2023-06-16 |
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bioconductor-impulsede
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public |
Detection of DE genes in time series data using impulse models
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2023-06-16 |
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hulk
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public |
Histosketching Using Little Kmers
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2023-06-16 |
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r-bedr
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public |
Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
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2023-06-16 |
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bioconductor-deds
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public |
Differential Expression via Distance Summary for Microarray Data
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2023-06-16 |
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bioconductor-phenodist
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public |
PhenoDist is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters.
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2023-06-16 |
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bioconductor-methyanalysis
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public |
DNA methylation data analysis and visualization
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2023-06-16 |
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r-traminer
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public |
Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe 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 simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
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2023-06-16 |
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bioconductor-swimr
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public |
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
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2023-06-16 |
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bioconductor-spotsegmentation
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public |
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
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2023-06-16 |
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bioconductor-mqtl.nmr
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public |
mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data. Distinctive features include normalisation using most-used approaches, peak alignment using RSPA approach, dimensionality reduction using SRV and binning approaches, and mQTL analysis for animal and human cohorts.
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2023-06-16 |
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r-nabor
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public |
An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D)
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2023-06-16 |
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r-taxa
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public |
Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data.
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2023-06-16 |
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vcf-annotator
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public |
Use the reference GenBank file to add biological annotations to the variant calls in a VCF.
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2023-06-16 |
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hotspot3d
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public |
This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed.
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2023-06-16 |
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clust
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public |
Optimised consensus clustering of multiple heterogeneous datasets.
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2023-06-16 |
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kipoiseq
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public |
kipoiseq: sequence-based data-laoders for Kipoi
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2023-06-16 |
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bioconductor-rpsixml
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public |
R interface to PSI-MI 2.5 files
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2023-06-16 |
