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perl-math-utils
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public |
Useful mathematical functions not in Perl
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2023-06-16 |
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dropletutils-scripts
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public |
CLI scripts for the DropletUtils package
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2023-06-16 |
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bioconductor-wavetiling
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public |
Wavelet-Based Models for Tiling Array Transcriptome Analysis
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2023-06-16 |
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snver
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public |
SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data.
It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.
Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation.
SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data.
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2023-06-16 |
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counterr
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public |
Counterr is a light-weight command line tool that computes errors in sequencing data by comparing the reads to a reference genome.
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2023-06-16 |
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bioconductor-stan
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public |
The Genomic STate ANnotation Package
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2023-06-16 |
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cromwell-tools
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public |
Utilities for interacting with the Cromwell workflow engine
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2023-06-16 |
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r-seurat-scripts
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public |
A set of wrappers for individual components of the Seurat package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
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2023-06-16 |
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bioconductor-geneselector
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public |
The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.
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2023-06-16 |
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bioconductor-bridge
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public |
Bayesian Robust Inference for Differential Gene Expression
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2023-06-16 |
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bioconductor-inversion
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public |
Inversions in genotype data
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2023-06-16 |
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bioconductor-cnvtools
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public |
A package to test genetic association with CNV data
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2023-06-16 |
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rvtests
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public |
Rare variant test software for next generation sequencing data
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2023-06-16 |
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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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2023-06-16 |
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var-agg
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public |
A simple helper for aggregating multi-sample VCF files into "site VCF" files.
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2023-06-16 |
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pyaavf
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public |
An amino acid variant format parser for Python.
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2023-06-16 |
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medpy
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public |
Medical image processing in Python
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2023-06-16 |
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metaquantome
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public |
Quantitative metaproteomics analysis of taxonomy and function.
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2023-06-16 |
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metawrap
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public |
MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
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2023-06-16 |
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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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2023-06-16 |
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kipoi_veff
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public |
kipoi_veff: variant effect prediction plugin for Kipoi
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2023-06-16 |
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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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2023-06-16 |
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python-sortedcontainers
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public |
sorted collections library, written in pure-Python, and fast as C-extensions
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2023-06-16 |
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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 |
