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swipe
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public |
Tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.
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2025-04-22 |
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wisecondorx
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public |
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
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2025-04-22 |
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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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2025-04-22 |
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r-sbpiper
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public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
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2025-04-22 |
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womtool
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public |
Command line utilities for interacting with WDL
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2025-04-22 |
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r-biodb
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public |
An R package for connecting to chemical and biological databases.
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2025-04-22 |
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migrate-n
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public |
Population Genetics - Panmixia and Migration detection
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2025-04-22 |
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fastspar
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public |
Rapid and scalable correlation estimation for compositional data
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2025-04-22 |
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r-rapidr
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public |
Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA
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2025-04-22 |
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r-propcis
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public |
Computes two-sample confidence intervals for single, paired and independent proportions.
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2025-04-22 |
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esimsa
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public |
Simple deconvolution of electrospray ionization peak lists
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2025-04-22 |
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ngmerge
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public |
Merging paired-end reads and removing sequencing adapters.
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2025-04-22 |
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bioconductor-mspuritydata
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public |
Fragmentation spectral libraries and data to test the msPurity package
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2025-04-22 |
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bsmap
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public |
BSMAP is a short reads mapping software for bisulfite sequencing reads.
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2025-04-22 |
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cortex_con
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public |
cortex_con (primary contact Mario Caccamo) is for consensus genome assembly
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2025-04-22 |
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prophasm
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public |
ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
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2025-04-22 |
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r-seqminer
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public |
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
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2025-04-22 |
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cdna_cupcake
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public |
cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
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2025-04-22 |
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gtfparse
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public |
GTF Parsing
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2025-04-22 |
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mirge
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public |
comprehensive analysis of miRNA sequencing data
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2025-04-22 |
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erds
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public |
Inferring copy number variants in high-coverage human genomes with next-generation sequencing data.
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2025-04-22 |
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lorikeet
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public |
Tool for digital spoligotyping of MTB strains from Illumina read data
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2025-04-22 |
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spotyping
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public |
SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
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2025-04-22 |
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blobtools
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public |
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
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2025-04-22 |
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r-genometricorr
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public |
Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
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2025-04-22 |
