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bamm
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public |
Metagenomics-focused BAM file manipulation
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2023-06-16 |
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perl-bio-cigar
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public |
Parse CIGAR strings and translate coordinates to/from reference/query
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2023-06-16 |
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cmv
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public |
A collection of tools for the visualisation of Hidden Markov Models (HMMV) and RNA-family models (CMV).
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2023-06-16 |
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perl-term-progressbar
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public |
provide a progress meter on a standard terminal
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2023-06-16 |
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perl-types-standard
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public |
bundled set of built-in types for Type::Tiny
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2023-06-16 |
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perl-pod-usage
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public |
print a usage message from embedded pod documentation
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2023-06-16 |
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qcumber
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public |
Quality control, quality trimming, adapter removal and sequence content check of NGS data.
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2023-06-16 |
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abruijn
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public |
Long read assembly via A-Bruijn graph
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2023-06-16 |
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bumbershoot
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public |
The Bumbershoot tool suite for analyzing shotgun proteomic data
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2023-06-16 |
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virema
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public |
ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.
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2023-06-16 |
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breakseq2
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public |
BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.
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2023-06-16 |
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chemfp
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public |
chemfp is a set of command-lines tools for generating cheminformatics fingerprints and searching those
fingerprints by Tanimoto similarity, as well as a Python library which can be used to build new tools.
These algorithms are designed for the dense, 100-10,000 bit
fingerprints which occur in small-molecule/pharmaceutical
chemisty. The Tanimoto search algorithms are implemented in C for
performance and support both threshold and k-nearest searches.
Fingerprint generation can be done either by extracting existing
fingerprint data from an SD file or by using an existing chemistry
toolkit. chemfp supports the Python libraries from Open Babel,
OpenEye, and RDKit toolkits.
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2023-06-16 |
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ig-flowtools
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public |
set of tools for flow cytometry analysis
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2023-06-16 |
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ig-checkflowtypes
|
public |
quick flow-related datatype for galaxy checks
|
2023-06-16 |
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perl-digest-md5-file
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public |
Perl extension for getting MD5 sums for files and urls.
|
2023-06-16 |
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clustergrammer
|
public |
A python module for the Clustergrammer visualization project
|
2023-06-16 |
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validate-fasta-database
|
public |
Code for Galaxy tool for quality control on FASTA database
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2023-06-16 |
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itsx
|
public |
ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi.
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2023-06-16 |
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samsift
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public |
Advanced filtering and tagging of SAM/BAM alignments using Python expressions.
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2023-06-16 |
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orthomcl
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public |
Ortholog groups of protein sequences
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2023-06-16 |
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hichipper
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public |
Processing HiChIP data into loops.
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2023-06-16 |
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ebfilter
|
public |
EBFilter (Empirical Bayesian Mutation Filtering)
|
2023-06-16 |
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picopore
|
public |
A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.
|
2023-06-16 |
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mglex
|
public |
MGLEX - MetaGenome Likelihood EXtractor
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2023-06-16 |
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hclust2
|
public |
hclust2 is a handy tool for plotting heat-maps
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2023-06-16 |
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qtip
|
public |
A tandem simulation approach for accurately predicting read alignment
mapping qualities.
|
2023-06-16 |
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hera
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public |
hera is a bioinformatics tool that helps analyze RNA-seq data, providing base-to-base alignment BAM files, transcript abundance estimation, and fusion gene detection.
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2023-06-16 |
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translatorx
|
public |
Multiple alignment of nucleotide sequences guided by amino acid information
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2023-06-16 |
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perl-string-util
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public |
String::Util -- String processing utilities
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2023-06-16 |
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perl-number-misc
|
public |
Number::Misc - handy utilities for numbers
|
2023-06-16 |
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maker
|
public |
MAKER is a portable and easily configurable genome annotation pipeline.
|
2023-06-16 |
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plant_tribes_assembly_post_processor
|
public |
Transcriptome assembly post processing pipeline
|
2023-06-16 |
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perl-test-toolbox
|
public |
Test::Toolbox - tools for testing
|
2023-06-16 |
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semeta
|
public |
SeMeta is a new software for taxonomic assignment of metagenomic reads. It
supports both single-end and paired-end reads. The software is implemented
in C++
|
2023-06-16 |
|
enasearch
|
public |
A Python library for interacting with ENA's API
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2023-06-16 |
|
irida-linker
|
public |
The NGS Archive Linker is a Perl script used to generate a structure of links for files stored in the IRIDA platform.
|
2023-06-16 |
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daisysuite
|
public |
DaisySuite - mapping-based pipeline for horizontal gene transfer (HGT) detection using sequencing data
|
2023-06-16 |
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probamconvert
|
public |
proBAMconvert is a conversion tool to convert common peptide identification files (mzIdentML, pepXML, mzTAB) to the proBAM or proBED format
|
2023-06-16 |
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bioconductor-mvgst
|
public |
mvGST provides platform-independent tools to identify GO terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. Given a matrix of one-sided p-values (rows for genes, columns for contrasts), mvGST uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify each gene set as being significantly more active (1), less active (-1), or not significantly differentially active (0) in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile.
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2023-06-16 |
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bpp-core
|
public |
Bio++ is a set of C++ libraries for Bioinformatics.
|
2023-06-16 |
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irep
|
public |
calculate iRep replication rates from metagenome sequencing
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2023-06-16 |
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plant_tribes_gene_family_classifier
|
public |
Gene family classifier pipeline
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2023-06-16 |
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tadarida-c
|
public |
Tadarida-C (Toolbox for Animal Detection on Acoustic Recordings - Classification part) for Galaxy use.
|
2023-06-16 |
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bioconductor-meshsim
|
public |
Provide for measuring semantic similarity over MeSH headings and MEDLINE documents
|
2023-06-16 |
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bioconductor-mmnet
|
public |
This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.
|
2023-06-16 |
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askocli
|
public |
Command line interface for a distant AskOmics
|
2023-06-16 |
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schavott
|
public |
Assembly and scaffolding of bacterial genomes in real time using MinION-sequencing.
|
2023-06-16 |
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mira
|
public |
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)
|
2023-06-16 |
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google-cloud-sdk
|
public |
Command-line interface for Google Cloud Platform products and services
|
2023-06-16 |
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r-downloader
|
public |
Provides a wrapper for the download.file function, making it possible to download files over HTTPS on Windows, Mac OS X, and other Unix-like platforms. The RCurl package provides this functionality (and much more) but can be difficult to install because it must be compiled with external dependencies. This package has no external dependencies, so it is much easier to install.
|
2023-06-16 |
