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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 |
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mlrho
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public |
Takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, , the sequencing error , the zygosity correlation, and the population recombination rate.
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2025-04-22 |
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krocus
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public |
krocus performs multi-locus sequence typing from uncorrected long reads.
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2025-04-22 |
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r-scimpute
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public |
scImpute is accurate and robust imputation of single-cell RNA sequencing data.
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2025-04-22 |
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ctat-lncrna
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public |
ctat-lncrna uses slncky
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2025-04-22 |
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riboraptor
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public |
Python package to analyse ribosome profiling data
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2025-04-22 |
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jali
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public |
Alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.
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2025-04-22 |
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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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2025-04-22 |
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sfs_code
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public |
This article introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent). © The Author 2008. Published by Oxford University Press. All rights reserved.
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2025-04-22 |
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r-sigqc
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public |
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
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2025-04-22 |
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r-fmsb
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public |
Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
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2025-04-22 |
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dawg
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public |
DNA Assembly with Gaps (Dawg) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation.
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2025-04-22 |
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seqyclean
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public |
Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
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2025-04-22 |
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fast5seek
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public |
Get paths for fast5 files contained in BAM, SAM, or fastq.
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2025-04-22 |
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forgi
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public |
RNA Graph Library
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2025-04-22 |
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dig2
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public |
dig2 is a simple but flexible in silico digester of protein sequences in the FASTA format. It allows for almost any enzyme to be simulated, including MS/MS enzymes to generate CID or ECD/ETD fragments.
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2025-04-22 |
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gretel
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public |
An algorithm for recovering haplotypes from metagenomes
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2025-04-22 |
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bibliospec
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public |
The BiblioSpec Spetral Library tool suite
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2025-04-22 |
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itero
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public |
A pipeline for iterative, guided contig assembly that integrates spades, bwa, and samtools to produce assembled contigs.
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2025-04-22 |
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rnaclust
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public |
A tool for clustering of RNAs based on their secondary structures using LocARNA
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2025-04-22 |
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biopet-vcfstats
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public |
Vcfstats is a tool that can generate metrics from a vcf file.
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2025-04-22 |
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bioconductor-interest
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public |
Intron-Exon Retention Estimator
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2025-04-22 |
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mustang
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public |
Mustang is a program that implements an algorithm for structural alignment of multiple protein structures.
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2025-04-22 |
