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dfam
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public |
The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes
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2025-04-22 |
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ncbi-genome-download
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public |
Download genome files from the NCBI FTP server.
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2025-04-22 |
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requests-mock
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public |
Mock out responses from the requests package
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2025-04-22 |
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minced
|
public |
MinCED - Mining CRISPRs in Environmental Datasets
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2025-04-22 |
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bioconductor-pcamethods
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public |
A collection of PCA methods
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2025-04-22 |
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soapec
|
public |
a correction tool for SOAPdenovo
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2025-04-22 |
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tophat-recondition
|
public |
Post-processor for TopHat unmapped reads
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2025-04-22 |
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r-scrm
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public |
A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
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2025-04-22 |
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r-giant
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public |
Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
|
2025-04-22 |
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r-solarius
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public |
SOLAR is the standard software program to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. This package allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. See <http://solar.txbiomedgenetics.org/> for more information about SOLAR.
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2025-04-22 |
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trinculo
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public |
A toolkit for carrying out genetic association for
multi-category phenotypes. Implements multinomial and ordinal
association incorporating covariates, conditional analysis,
empirical and non-emperical priors and fine-mapping.
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2025-04-22 |
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debwt
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public |
A efficient method to construct BWT index of a given DNA sequence, especially
useful for gigantic and high similar genome.
DeBWT has good scalability to construct BWT in parallel computing.
It is well-suited to run on multiple core servers or clusters to
construct the BWT of large collections of genome sequences.
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2025-04-22 |
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medusa-data-fusion
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public |
Medusa is an approach to detect size-k modules of objects that, taken together,
appear most significant to another set of objects. It builds on collective
matrix factorization to derive different semantics, and it formulates the
growing of the modules as a submodular optimization program.
|
2025-04-22 |
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segway
|
public |
a tool for easy pattern discovery and identification in functional genomics data.
|
2025-04-22 |
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optbuild
|
public |
build command lines for external programs
|
2025-04-22 |
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backports.unittest_mock
|
public |
backports.unittest_mock
|
2025-04-22 |
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autolog
|
public |
quick and easy logging setup
|
2025-04-22 |
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forked-path
|
public |
An object oriented file path module
|
2025-04-22 |
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textinput
|
public |
streamlined version of stdlib fileinput
|
2025-04-22 |
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gmtk
|
public |
A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)
|
2025-04-22 |
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optplus
|
public |
additional options for optparse
|
2025-04-22 |
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soapdenovo2-errorcorrection
|
public |
Error correction for soapdenovo2.
|
2025-04-22 |
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soapdenovo2-prepare
|
public |
SoapDenovo2 Data prepare module using assembled contig to do scaffold assembly
|
2025-04-22 |
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genblastg
|
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.
|
2025-04-22 |
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genblasta
|
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.
|
2025-04-22 |
