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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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2025-04-22 |
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r-george
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public |
geoRge, a computational tool for stable isotope labelling detection in LC/MS-based untargeted metabolomics
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2025-04-22 |
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ascat
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public |
ASCAT is a method to derive copy number profiles of tumour cells,
accounting for normal cell admixture and tumour aneuploidy (Figure 1).
ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the
amount of DNA per tumour cell, expressed as multiples of haploid genomes)
from SNP array or massively parallel sequencing data, and calculates
whole-genome allele-specific copy number profiles (the number of copies of
both parental alleles for all SNP loci across the genome).
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2025-04-22 |
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structure
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public |
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
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2025-04-22 |
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perl-digest-md5-file
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public |
Perl extension for getting MD5 sums for files and urls.
|
2025-04-22 |
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breakseq2
|
public |
BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.
|
2025-04-22 |
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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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2025-04-22 |
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qcumber
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public |
Quality control, quality trimming, adapter removal and sequence content check of NGS data.
|
2025-04-22 |
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bioconductor-methylumi
|
public |
Handle Illumina methylation data
|
2025-04-22 |
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abruijn
|
public |
Long read assembly via A-Bruijn graph
|
2025-04-22 |
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ig-checkflowtypes
|
public |
quick flow-related datatype for galaxy checks
|
2025-04-22 |
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bioconductor-ggcyto
|
public |
Visualize Cytometry data with ggplot
|
2025-04-22 |
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bioconductor-flowworkspace
|
public |
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
|
2025-04-22 |
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bioconductor-ncdfflow
|
public |
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
|
2025-04-22 |
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bioconductor-flowsom
|
public |
Using self-organizing maps for visualization and interpretation of cytometry data
|
2025-04-22 |
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bioconductor-flowutils
|
public |
Utilities for flow cytometry
|
2025-04-22 |
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rmats2sashimiplot
|
public |
rmats2sashimiplot
|
2025-04-22 |
|
bioconductor-fdb.infiniummethylation.hg19
|
public |
Compiled HumanMethylation27 and HumanMethylation450 annotations
|
2025-04-22 |
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clustergrammer
|
public |
A python module for the Clustergrammer visualization project
|
2025-04-22 |
|
afterqc
|
public |
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats.
|
2025-04-22 |
|
connor
|
public |
A command-line tool to deduplicate bam files based on custom, inline barcoding.
|
2025-04-22 |
|
muse
|
public |
An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples.
|
2025-04-22 |
|
validate-fasta-database
|
public |
Code for Galaxy tool for quality control on FASTA database
|
2025-04-22 |
|
quasitools
|
public |
Quasitools is a collection of tools for analysing Viral Quasispecies
|
2025-04-22 |
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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.
|
2025-04-22 |
