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kat
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public |
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts
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2023-06-16 |
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mobster
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public |
NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data, see Thung et al. Genome Biol. 2014 for more information.
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2023-06-16 |
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metfrag
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public |
MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecular structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.
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2023-06-16 |
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ribocode
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public |
A package for detecting the actively translated ORFs using ribosome-profiling data
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2023-06-16 |
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prosolo
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public |
A highly sensitive and accurate Bayesian caller for variants in single cell sequencing data.
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2023-06-16 |
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perl-module-load-conditional
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public |
Looking up module information / loading at runtime
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2023-06-16 |
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edlib
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public |
C/C++ library and program for sequence alignment using edit (Levenshtein) distance
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2023-06-16 |
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genblastg
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public |
genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.
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2023-06-16 |
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iva
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public |
Iterative Virus Assembler
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2023-06-16 |
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r-histonehmm
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public |
histoneHMM is a software to analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples
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2023-06-16 |
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wub
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public |
Tools and software library developed by the ONT Applications group
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2023-06-16 |
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minvar
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public |
A tool to detect minority variants in HIV-1 and HCV populations
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2023-06-16 |
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nextgenmap
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public |
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.
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2023-06-16 |
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nudup
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public |
Marks/removes duplicate molecules based on the molecular tagging technology used in NuGEN products.
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2023-06-16 |
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python-omero
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public |
Client library offering helper methods to access an OMERO server.
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2023-06-16 |
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dia_umpire
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public |
DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA)
mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation
using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.
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2023-06-16 |
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tbl2asn
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public |
tbl2asn is a program that automates the creation of sequence records for submission to GenBank
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2023-06-16 |
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pyrad
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public |
Assembly and analysis of RADseq data sets
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2023-06-16 |
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roary
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public |
Rapid large-scale prokaryote pan genome analysis
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2023-06-16 |
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manorm
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public |
A robust model for quantitative comparison of ChIP-Seq data sets.
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2023-06-16 |
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kobas
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public |
KEGG Orthology Based Annotation System
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2023-06-16 |
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dx-cwl
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public |
Import and run CWL workflows on DNAnexus
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2023-06-16 |
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nanolyse
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public |
Removing lambda DNA control reads from fastq dataset
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2023-06-16 |
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moff
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public |
moFF is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides.
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2023-06-16 |
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pauvre
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public |
Tools for plotting Oxford Nanopore and other long-read data.
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2023-06-16 |
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stringmlst
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public |
Fast k-mer based tool for multi locus sequence typing (MLST) directly from genome sequencing reads
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2023-06-16 |
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fastlmm
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public |
Fast GWAS
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2023-06-16 |
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r-biomark
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public |
Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.
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2023-06-16 |
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seroba
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public |
SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references.
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2023-06-16 |
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intervene
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public |
A tool for intersection of multiple gene or genomic region sets and visualization as venn diagrams, UpSet plots or pariwaise heatmaps
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2023-06-16 |
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perl-http-server-simple
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public |
Lightweight HTTP server
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2023-06-16 |
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a5-miseq
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public |
A5-miseq is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_
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2023-06-16 |
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break-point-inspector
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public |
BPI uses Manta’s variant calls to re-analyse BAM files and precisely determine the location of the breaks, and applies a set of filters to remove false positives, thereby increasing the accuracy of Manta’s calls.
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2023-06-16 |
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perl-moosex-app
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public |
Write user-friendly command line apps with even less suffering
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2023-06-16 |
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r-purbayes
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public |
PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
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2023-06-16 |
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r-icluster
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public |
Integrative clustering of multiple genomic data types using a joint latent variable model.
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2023-06-16 |
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haystack_bio
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public |
Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
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2023-06-16 |
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srst2
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public |
No Summary
|
2023-06-16 |
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r-mixomics
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public |
Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.
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2023-06-16 |
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wdltool
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public |
Command line utilities for interacting with WDL
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2023-06-16 |
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watchdog-wms
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public |
Watchdog, a WMS for the automated and distributed analysis of large-scale experimental data. The software is implemented in Java and is thus platform-independent. Main feature include + straightforward processing of replicate data + support for distributed computer systems + remote storage support + customizable error detection + manual intervention into workflow execution + GUI for workflow construction using pre-defined modules + a helper script for creating new module definitions + no restriction to specific programming languages + provides a flexible plugin system for extending without modifying the original sources
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2023-06-16 |
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seq-seq-pan
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public |
seq-seq-pan
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2023-06-16 |
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repenrich
|
public |
RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
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2023-06-16 |
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perl-moose
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public |
A postmodern object system for Perl 5
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2023-06-16 |
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sicer
|
public |
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
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2023-06-16 |
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panx
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public |
Microbial pan-genome analysis and exploration tool
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2023-06-16 |
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perl-go-perl
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public |
perl modules for GO and other OBO ontologies
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2023-06-16 |
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r-smvar
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public |
Implements the structural model for variances in order to detect differentially expressed genes from gene expression data
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2023-06-16 |
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pneumocat
|
public |
PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)
|
2023-06-16 |
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r-metarnaseq
|
public |
Implementation of two p-value combination techniques (inverse normal and Fisher methods). A vignette is provided to explain how to perform a meta-analysis from two independent RNA-seq experiments.
|
2023-06-16 |
