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ucsc-sqltoxml
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public |
dump out all or part of a relational database to XML, guided
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2024-12-11 |
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genrich
|
public |
Detecting sites of genomic enrichment.
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2024-12-11 |
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pardre
|
public |
ParDRe is a parallel tool to remove duplicate reads.
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2024-12-11 |
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clearcut
|
public |
The reference implementation for Relaxed Neighbor Joining (RNJ).
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2024-12-11 |
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r-ccube
|
public |
R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data.
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2024-12-11 |
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r-disprose
|
public |
Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.
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2024-12-11 |
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r-abdiv
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public |
Alpha and Beta Diversity Measures
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2024-12-11 |
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ucsc-fafilter
|
public |
Filter fa records, selecting ones that match the specified conditions
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2024-12-11 |
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tadarida-d
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public |
Tadarida-D (Toolbox for Animal Detection on Acoustic Recordings - Detection and Feature extraction part) for Galaxy use.
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2024-12-11 |
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autodock
|
public |
AutoDock is a suite of automated docking tools.
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2024-12-11 |
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mfqe
|
public |
mfqe is a tool for quickly seperating fasta and fastq files
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2024-12-11 |
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pyrle
|
public |
Genomic Rle-objects for Python
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2024-12-11 |
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ucsc-getrna
|
public |
Get mrna for GenBank or RefSeq sequences found in a database
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2024-12-11 |
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ucsc-hgloadsqltab
|
public |
Load table into database from SQL and text files.
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2024-12-11 |
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ucsc-faonerecord
|
public |
Extract a single record from a .FA file
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2024-12-11 |
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bx-python
|
public |
Tools for manipulating biological data, particularly multiple sequence alignments
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2024-12-11 |
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dig2
|
public |
dig2 is a simple but flexible in silico digester of protein sequences in the FASTA format. It allows for almost any enzyme to be simulated, including MS/MS enzymes to generate CID or ECD/ETD fragments.
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2024-12-11 |
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ssu-align
|
public |
SSU-ALIGN: structural alignment of SSU rRNA sequences
|
2024-12-11 |
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occultercut
|
public |
A package for measuring the local GC-content bias in genomes and fungal species
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2024-12-11 |
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samcut
|
public |
samcut is `cut` for sam. Select (cut) columns from the output of `samtools view` using human-readale field names.
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2024-12-11 |
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pandaseq
|
public |
No Summary
|
2024-12-11 |
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solexaqa
|
public |
Quality statistics and visual representations for second-generation sequencing data
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2024-12-11 |
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sharg
|
public |
A modern argument parser for C++ tools.
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2024-12-11 |
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biodiff
|
public |
exact comparison of biological sequences
|
2024-12-11 |
|
seq-hasher
|
public |
Compute hash digests for DNA sequences in a FASTA file, with support for circular permutations
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2024-12-11 |
|
tr-trimmer
|
public |
Identify and trim terminal repeats from sequences in FASTA files
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2024-12-11 |
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unitig-caller
|
public |
Determines presence/absence of sequence elements in bacterial sequence data.
|
2024-12-11 |
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bioconductor-mpra
|
public |
Analyze massively parallel reporter assays
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2024-12-11 |
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pseqsid
|
public |
Calculates pairwise sequence identity, similarity and normalized similarity
score of proteins in a multiple sequence alignment.
|
2024-12-11 |
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pixelator
|
public |
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
|
2024-12-11 |
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exomiser-rest-prioritiser
|
public |
Exomiser prioritiser REST API
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2024-12-11 |
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civicpy
|
public |
CIViC variant knowledgebase analysis toolkit.
|
2024-12-11 |
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clark
|
public |
Fast, accurate and versatile k-mer based classification system
|
2024-12-10 |
|
seqstats
|
public |
Quick summary statistics on fasta/fastq(.gz) files
|
2024-12-10 |
|
roguenarok
|
public |
Phylogenetics - algorithm for the identification of rogue taxa in a tree set.
|
2024-12-10 |
|
guidescan
|
public |
GuideScan is a tool for genome-wide CRISPR guide RNA (gRNA) design and analysis in custom genomes.
|
2024-12-10 |
|
sherpas
|
public |
Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences.
|
2024-12-10 |
|
porechop
|
public |
Adapter removal and demultiplexing of Oxford Nanopore reads
|
2024-12-10 |
|
wfa2-lib
|
public |
Wavefront alignment algorithm library v2
|
2024-12-10 |
|
fermi-lite
|
public |
Fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size.
|
2024-12-10 |
|
sts-smctc
|
public |
A C++ template class library for the efficient and convenient implementation of very general Sequential Monte Carlo algorithms.
|
2024-12-10 |
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gecode
|
public |
Generic constraint development environment
|
2024-12-10 |
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ucsc-liftover
|
public |
Move annotations from one assembly to another
|
2024-12-10 |
|
vargeno
|
public |
Fast SNP genotyping tool for whole genome sequence data and large SNP database.
|
2024-12-10 |
|
treemix
|
public |
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
|
2024-12-10 |
|
libgff
|
public |
A simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase.
|
2024-12-10 |
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minirmd
|
public |
Remove duplicate and near-duplicate reads
|
2024-12-10 |
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soapdenovo2-prepare
|
public |
SoapDenovo2 Data prepare module using assembled contig to do scaffold assembly
|
2024-12-10 |
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ucsc-beditemoverlapcount
|
public |
count number of times a base is overlapped by the
|
2024-12-10 |
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mindthegap
|
public |
MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation.
|
2024-12-10 |
