|
genomestrip
|
public |
Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using whole-genome sequencing data
|
2025-04-22 |
|
r-ngsplotdb-hg38
|
public |
HG19 genome database for NGSplot
|
2025-04-22 |
|
r-ngsplotdb-hg19
|
public |
HG19 genome database for NGSplot
|
2025-04-22 |
|
r-ngsplotdb-mm10
|
public |
MM10 genome database for NGSplot
|
2025-04-22 |
|
ngsplotdb-ngsplotdb-hg19
|
public |
HG19 genome database for NGSplot
|
2025-04-22 |
|
r-ngsplot
|
public |
Quick mining and visualization of NGS data by integrating genomic databases
|
2025-04-22 |
|
biopet-sampleconfig
|
public |
#### Tools - ExtractTsv This mean can extract samples, libraries and readgroups from a sample config file.
|
2025-04-22 |
|
r-kinship2
|
public |
Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
|
2025-04-22 |
|
verifybamid2
|
public |
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
|
2025-04-22 |
|
phyluce
|
public |
Software for UCE (and general) phylogenomics.
|
2025-04-22 |
|
confindr
|
public |
Detect intra- and inter-species bacterial contamination in NGS reads.
|
2025-04-22 |
|
bam2fastx
|
public |
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
|
2025-04-22 |
|
pbcopper
|
public |
Core C++ library for data structures, algorithms, and utilities
|
2025-04-22 |
|
pathwaymatcher
|
public |
PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome.
|
2025-04-22 |
|
pisces
|
public |
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
|
2025-04-22 |
|
logol
|
public |
Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic)
|
2025-04-22 |
|
kipoi
|
public |
Kipoi: model zoo for genomics
|
2025-04-22 |
|
bcov
|
public |
BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence.
|
2025-04-22 |
|
r-taxa
|
public |
Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data.
|
2025-04-22 |
|
r-funrar
|
public |
Computes functional rarity indices as proposed by Violle et al. (2017)
|
2025-04-22 |
|
meta-sparse
|
public |
SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to predict origins of metagenomic reads.
|
2025-04-22 |
|
ncbi-vdb
|
public |
SRA tools database engine.
|
2025-04-22 |
|
super-focus
|
public |
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
|
2025-04-22 |
|
r-sigtree
|
public |
Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.
|
2025-04-22 |
|
r-phyext2
|
public |
Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
|
2025-04-22 |
