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amptk
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public |
AMPtk: Amplicon tool kit for processing high throughput amplicon sequencing data.
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2023-11-07 |
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blastbesties
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public |
Rapid discovery of reciprocal best blast pairs from BLAST output files.
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2023-11-07 |
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nmrml2isa
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public |
nmrml2isa - nmrML to ISA-Tab parsing tool
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2023-11-07 |
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catch
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public |
A package for designing compact and comprehensive capture probe sets.
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2023-11-01 |
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bismark
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public |
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
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2023-10-26 |
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microhapdb
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public |
Portable database of microhaplotype marker and allele frequency data.
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2023-10-25 |
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arvados-cwl-runner
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public |
Arvados Common Workflow Language runner
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2023-10-25 |
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uropa
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public |
UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for genomic region annotation from e.g. peak calling.
It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction and strand into account.
Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding.
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2023-10-22 |
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cromshell
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public |
Command-line interface to the Cromwell workflow manager
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2023-10-17 |
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fcsparser
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public |
A python package for reading raw fcs files
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2023-10-17 |
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snpsift
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public |
Toolbox that allows you to filter and manipulate annotated files
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2023-10-17 |
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asciigenome
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public |
Command-line genome browser running from terminal window and solely based on ASCII characters
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2023-10-08 |
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ksw
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public |
Ksw: (interactive) smith-waterman in C
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2023-10-04 |
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ribotish
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public |
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
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2023-09-25 |
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prokka
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public |
Rapid annotation of prokaryotic genomes
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2023-09-23 |
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nanoget
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public |
Functions to extract information from Oxford Nanopore sequencing data and alignments.
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2023-09-19 |
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isatools
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public |
Metadata tracking tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments
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2023-09-12 |
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microbecensus
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public |
A command-line tool for estimating average genome size from shotgun sequence data
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2023-09-10 |
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trinotate
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public |
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms
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2023-09-09 |
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varscan
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public |
variant detection in massively parallel sequencing data
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2023-09-09 |
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taxtastic
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public |
Tools for taxonomic naming and annotation
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2023-09-06 |
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dr-disco
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public |
Dr. Disco: fusion gene and genomic breakpoint detection in random hexamer RNA-seq data
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2023-09-06 |
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asqcan
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public |
A combined pipeline for bacterial genome assembly, quality control and annotation
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2023-09-05 |
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digestiflow-demux
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public |
Digestiflow Command Line Client.
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2023-09-04 |
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mtbseq
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public |
Pipeline for WGS analysis of M. tuberculosis
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2023-08-24 |
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eggnog-mapper
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public |
Fast genome-wide functional annotation through orthology assignment.
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2023-08-18 |
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mapdamage2
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public |
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences http://geogenetics.ku.dk/all_literature/mapdamage/
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2023-08-17 |
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perl-module-scandeps
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public |
Recursively scan Perl code for dependencies
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2023-08-04 |
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pythomics
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public |
A multi-omic python package
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2023-08-04 |
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ncbi-genome-download
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public |
Download genome files from the NCBI FTP server.
|
2023-08-01 |
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rgt
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public |
Toolkit to perform regulatory genomics data analysis
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2023-07-31 |
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crimson
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public |
Bioinformatics tool outputs converter to JSON or YAML.
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2023-07-29 |
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metaxa
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public |
Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.
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2023-07-25 |
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bioconductor-interactivedisplay
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public |
Package for enabling powerful shiny web displays of Bioconductor objects
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2023-07-23 |
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r-dgeclustering
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public |
DGEclustering is an R package for multidimensional clustering of differential gene expression datasets, and it integrates GO annotations to improve the clustering result.
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2023-07-19 |
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bioconductor-singlecellexperiment-scripts
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public |
A set of wrappers for operations associated with the SingleCellExperiment package. Functions in 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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2023-07-18 |
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bioconductor-cancersubtypes
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public |
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
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2023-07-18 |
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bioconductor-crisprseekplus
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public |
crisprseekplus
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2023-07-18 |
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r-breakaway
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public |
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, as well as the most commonly used estimates. Methods uniquely available in this package include objective Bayes estimators described in Barger and Bunge (2010) <doi:10.1214/10-BA527>, frequency-ratio-based estimators described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, and as described in Willis, Whitman, and Bunge (2016) <doi:10.1111/rssc.12206>, a linear modeling approach for detecting changes in diversity.
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2023-07-17 |
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r-sigtree
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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.
|
2023-07-17 |
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r-metalonda
|
public |
Identify time intervals of differentially abundant metagenomics features in longitudinal studies.
|
2023-07-17 |
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bioconductor-refplus
|
public |
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
|
2023-07-17 |
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bioconductor-metab
|
public |
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
|
2023-07-17 |
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transdecoder
|
public |
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
|
2023-07-16 |
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r-dartr
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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.
|
2023-07-16 |
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perl-file-listing
|
public |
parse directory listing
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2023-07-16 |
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bioconductor-sispa
|
public |
SISPA: Method for Sample Integrated Set Profile Analysis
|
2023-07-15 |
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fastphylo
|
public |
Fastphylo is software project containing the implementations of the algorithms "Fast Computation of Distance Estimators" and "Fast Neighbor Joining".
|
2023-07-15 |
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bioconductor-genbankr
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public |
Parsing GenBank files into semantically useful objects
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2023-07-14 |
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bioconductor-alpine
|
public |
alpine
|
2023-07-14 |
