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libstatgen
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public |
Useful set of classes for creating statistical genetic programs.
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2025-03-25 |
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bgreat
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public |
BGREAT2 is a read mapping tool for NGS sequencing data that align reads on a de Bruijn graph. Preliminary version described at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1103-9 and used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)
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2025-03-25 |
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iced
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public |
The python module iced implements the ICE normalization of hic data.
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2025-03-25 |
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btrim
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public |
This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)
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2025-03-25 |
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bioexcel_seqqc
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public |
Sequence Quality Control pipeline/modules
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-breakaway
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public |
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, as well as the most commonly used estimates. Methods uniquely available in this package include objective Bayes estimators described in Barger and Bunge (2010) <doi:10.1214/10-BA527>, frequency-ratio-based estimators described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, and as described in Willis, Whitman, and Bunge (2016) <doi:10.1111/rssc.12206>, a linear modeling approach for detecting changes in diversity.
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2025-03-25 |
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mhcflurry
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public |
MHC Binding Predictor
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2025-03-25 |
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mhcnames
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public |
Python library for MHC nomenclature parsing
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2025-03-25 |
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metawrap
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public |
MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
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2025-03-25 |
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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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2025-03-25 |
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bioconductor-deqms
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public |
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
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2025-03-25 |
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gvcfgenotyper
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public |
A utility for merging and genotyping Illumina-style GVCFs.
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2025-03-25 |
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r-nam
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public |
Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
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2025-03-25 |
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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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2025-03-25 |
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changeo
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public |
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data. Citations: Gupta, et al (2015) <doi:10.1093/bioinformatics/btv359>.
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2025-03-25 |
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r-loom
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public |
An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files.
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2025-03-25 |
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nimnexus
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public |
command-line tools for processing ChIP-nexus data
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2025-03-25 |
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airr
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public |
AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data. Citations: AIRR standards <doi:10.5281/zenodo.1185414>.
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2025-03-25 |
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r-tigger
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public |
Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>.
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2025-03-25 |
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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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2025-03-25 |
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perl-findbin-real
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public |
Locates the full path to the script bin directory to allow the use of paths relative to the bin directory.
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2025-03-25 |
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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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2025-03-25 |
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ncrf
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public |
Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data.
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2025-03-25 |
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blockclust
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public |
Efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
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2025-03-25 |
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deeptoolsintervals
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public |
A python module creating/accessing GTF-based interval trees with associated meta-data
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2025-03-25 |
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perl-clone-choose
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public |
Choose appropriate clone utility
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2025-03-25 |
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r-lncpipereporter
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public |
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
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2025-03-25 |
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r-classdiscovery
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public |
Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.
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2025-03-25 |
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cocoscore
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public |
CoCoScore: context-aware co-occurrence scores for biomedical text mining applications
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2025-03-25 |
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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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2025-03-25 |
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wgfast
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public |
The whole genome focused array SNP typing (WG-FAST) pipeline
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2025-03-25 |
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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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2025-03-25 |
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demuxlet
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public |
Genetic multiplexing of barcoded single cell RNA-seq
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2025-03-25 |
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parasail-python
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public |
Python bindings for the parasail C library containing implementations of pairwise sequence alignment algorithms.
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2025-03-25 |
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rgt
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public |
Toolkit to perform regulatory genomics data analysis
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2025-03-25 |
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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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2025-03-25 |
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cgat-daisy
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public |
A system to design and execute benchmarks
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2025-03-25 |
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codingquarry
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public |
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
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2025-03-25 |
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comet-ms
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public |
Comet is a command line tool that does MS/MS database search.
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2025-03-25 |
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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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2025-03-25 |
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bcftools-gtc2vcf-plugin
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public |
Tools to convert Illumina and Affymetrix array intensity data files into VCF files.
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2025-03-25 |
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kipoiseq
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public |
kipoiseq: sequence-based data-laoders for Kipoi
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2025-03-25 |
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kipoi_veff
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public |
kipoi_veff: variant effect prediction plugin for Kipoi
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2025-03-25 |
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r-goeveg
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public |
A collection of functions useful in (vegetation) community analyses and ordinations, mainly to facilitate plotting and interpretation. Includes automatic species selection for ordination diagrams, species response curves and rank-abundance curves.
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2025-03-25 |
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bioconductor-scrnaseq
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public |
Collection of Public Single-Cell RNA-Seq Datasets
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2025-03-25 |
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bioconductor-isee
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public |
Interactive SummarizedExperiment Explorer
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2025-03-25 |
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r-facets
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public |
Cellular Fraction and Copy Numbers from Tumor Sequencing
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2025-03-25 |
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bioconductor-decipher
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public |
Tools for curating, analyzing, and manipulating biological sequences
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2025-03-25 |
