|
bsmap
|
public |
BSMAP is a short reads mapping software for bisulfite sequencing reads.
|
2025-03-25 |
|
cortex_con
|
public |
cortex_con (primary contact Mario Caccamo) is for consensus genome assembly
|
2025-03-25 |
|
prophasm
|
public |
ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
|
2025-03-25 |
|
r-seqminer
|
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.
|
2025-03-25 |
|
cdna_cupcake
|
public |
cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
|
2025-03-25 |
|
gtfparse
|
public |
GTF Parsing
|
2025-03-25 |
|
mirge
|
public |
comprehensive analysis of miRNA sequencing data
|
2025-03-25 |
|
erds
|
public |
Inferring copy number variants in high-coverage human genomes with next-generation sequencing data.
|
2025-03-25 |
|
lorikeet
|
public |
Tool for digital spoligotyping of MTB strains from Illumina read data
|
2025-03-25 |
|
spotyping
|
public |
SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
|
2025-03-25 |
|
blobtools
|
public |
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
|
2025-03-25 |
|
stereogene
|
public |
StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
|
2025-03-25 |
|
r-genometricorr
|
public |
Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
|
2025-03-25 |
|
mlrho
|
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.
|
2025-03-25 |
|
krocus
|
public |
krocus performs multi-locus sequence typing from uncorrected long reads.
|
2025-03-25 |
|
r-scimpute
|
public |
scImpute is accurate and robust imputation of single-cell RNA sequencing data.
|
2025-03-25 |
|
ctat-lncrna
|
public |
ctat-lncrna uses slncky
|
2025-03-25 |
|
riboraptor
|
public |
Python package to analyse ribosome profiling data
|
2025-03-25 |
|
jali
|
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.
|
2025-03-25 |
|
livekraken
|
public |
LiveKraken is a real-time metagenomic classifier for Illumina sequencing data.
|
2025-03-25 |
|
r-shazam
|
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>.
|
2025-03-25 |
|
sfs_code
|
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.
|
2025-03-25 |
|
r-sigqc
|
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.
|
2025-03-25 |
|
r-fmsb
|
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.
|
2025-03-25 |
|
rcorrector
|
public |
Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.
|
2025-03-25 |
|
dawg
|
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.
|
2025-03-25 |
|
seqyclean
|
public |
Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
|
2025-03-25 |
|
fast5seek
|
public |
Get paths for fast5 files contained in BAM, SAM, or fastq.
|
2025-03-25 |
|
forgi
|
public |
RNA Graph Library
|
2025-03-25 |
|
dig2
|
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.
|
2025-03-25 |
|
gretel
|
public |
An algorithm for recovering haplotypes from metagenomes
|
2025-03-25 |
|
r-dartr
|
public |
Functions are provided that facilitate the import and analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.
|
2025-03-25 |
|
bibliospec
|
public |
The BiblioSpec Spetral Library tool suite
|
2025-03-25 |
|
itero
|
public |
A pipeline for iterative, guided contig assembly that integrates spades, bwa, and samtools to produce assembled contigs.
|
2025-03-25 |
|
rnaclust
|
public |
A tool for clustering of RNAs based on their secondary structures using LocARNA
|
2025-03-25 |
|
biopet-vcfstats
|
public |
Vcfstats is a tool that can generate metrics from a vcf file.
|
2025-03-25 |
|
yacrd
|
public |
Yet Another Chimeric Read Detector, with long-read mapper result as input.
|
2025-03-25 |
|
bioconductor-interest
|
public |
Intron-Exon Retention Estimator
|
2025-03-25 |
|
akt
|
public |
Ancestry and Kinship Tools (AKT)
|
2025-03-25 |
|
staramr
|
public |
Scan genome contigs against the ResFinder and PointFinder databases
|
2025-03-25 |
|
mustang
|
public |
Mustang is a program that implements an algorithm for structural alignment of multiple protein structures.
|
2025-03-25 |
|
perl-perl4-corelibs
|
public |
libraries historically supplied with Perl 4
|
2025-03-25 |
|
ac-diamond
|
public |
AC-DIAMOND is a DNA-protein alignment tool
|
2025-03-25 |
|
hanselx
|
public |
A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
|
2025-03-25 |
|
desman
|
public |
De novo Extraction of Strains from MetAgeNomes
|
2025-03-25 |
|
perl-socket
|
public |
networking constants and support functions
|
2025-03-25 |
|
r-stampp
|
public |
Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi
|
2025-03-25 |
|
r-pegas
|
public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
|
2025-03-25 |
|
r-qorts
|
public |
QoRTs toolkit for analysis, quality control, and data management of RNA-Seq
datasets.
|
2025-03-25 |
|
bioconductor-snprelate
|
public |
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
|
2025-03-25 |
