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discovardenovo
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public |
Suitable for de novo assembly of large and small genomes.
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2023-06-16 |
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quorum
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public |
No Summary
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2023-06-16 |
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r-splancs
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public |
The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
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2023-06-16 |
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r-sparql
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public |
Use SPARQL to pose SELECT or UPDATE queries to an end-point.
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2023-06-16 |
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r-docopt
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public |
Define a command-line interface by just giving it a description in the specific format.
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2023-06-16 |
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r-mba
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public |
Scattered data interpolation with Multilevel B-Splines
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2023-06-16 |
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r-rpmg
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public |
Really Poor Man's Graphical User Interface, used to create interactive R analysis sessions with simple R commands.
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2023-06-16 |
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r-rrcov
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public |
Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point.
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2023-06-16 |
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metavelvet-sl-pipeline
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public |
No Summary
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2023-06-16 |
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r-geomap
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public |
Set of routines for making Map Projections (forward and inverse), Topographic Maps, Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
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2023-06-16 |
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r-giant
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public |
Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
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2023-06-16 |
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r-rfoc
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public |
Graphics for statistics on a sphere, as applied to geological fault data, crystallography, earthquake focal mechanisms, radiation patterns, ternary plots and geographical/geological maps. Non-double couple plotting of focal spheres and source type maps are included for statistical analysis of moment tensors.
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2023-06-16 |
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r-rseis
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public |
Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
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2023-06-16 |
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r-permute
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public |
A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided.
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2023-06-16 |
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miranda
|
public |
An algorithm for finding genomic targets for microRNAs
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2023-06-16 |
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mgf-formatter
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public |
No Summary
|
2023-06-16 |
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piler
|
public |
PILER is public domain software for analyzing repetitive DNA found in genome sequences.
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2023-06-16 |
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perl-exporter
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public |
No Summary
|
2023-06-16 |
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genblasta
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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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neptune
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public |
No Summary
|
2023-06-16 |
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soapdenovo2
|
public |
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.
|
2023-06-16 |
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hivtrace
|
public |
HIV TRACE is an application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.
|
2023-06-16 |
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python-fakemp
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public |
Fake multiprocessing pool objects
|
2023-06-16 |
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forked-path
|
public |
An object oriented file path module
|
2023-06-16 |
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flock
|
public |
No Summary
|
2023-06-16 |
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soapdenovo2-gapcloser
|
public |
a tool named GapCloser for SOAPdenovo.
|
2023-06-16 |
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platypus-variant
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public |
A Haplotype-Based Variant Caller For Next Generation Sequence Data
|
2023-06-16 |
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bioconductor-fourcseq
|
public |
Package analyse 4C sequencing data
|
2023-06-16 |
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rtg-tools
|
public |
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
|
2023-06-16 |
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fastqc
|
public |
A quality control tool for high throughput sequence data.
|
2023-06-16 |
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vardict
|
public |
A sensitive variant caller for both single and paired sample variant calling
|
2023-06-16 |
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perl-pdf-api2
|
public |
Facilitates the creation and modification of PDF files
|
2023-06-16 |
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wham
|
public |
Structural variant detection and association testing
|
2023-06-16 |
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jellyfish
|
public |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
|
2023-06-16 |
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migmap
|
public |
A wrapper for IgBlast V-(D)-J mapping tool designed to facilitate analysis immune receptor libraries profiled using high-throughput sequencing.
|
2023-06-16 |
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weblogo
|
public |
WebLogo3 : Sequence Logos Redrawn
|
2023-06-16 |
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trimmomatic
|
public |
A flexible read trimming tool for Illumina NGS data
|
2023-06-16 |
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perl-dbi
|
public |
Database independent interface for Perl
|
2023-06-16 |
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r-bio3d
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public |
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
|
2023-06-16 |
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ipython-cluster-helper
|
public |
Tool to easily start up an IPython cluster on different schedulers
|
2023-06-16 |
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bioconductor-biocinstaller
|
public |
This package is used to install and update Bioconductor, CRAN, and (some) github packages.
|
2023-06-16 |
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metasv
|
public |
An accurate and integrative structural-variant caller for next generation sequencing
|
2023-06-16 |
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geneimpacts
|
public |
prioritize effects of variant annotations from VEP, SnpEff, et al.
|
2023-06-16 |
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r-ks
|
public |
Kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.
|
2023-06-16 |
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r-multicool
|
public |
A set of tools to permute multisets without loops or hash tables
and to generate integer partitions. The permutation functions are based on C code
from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm
is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix
Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The
permutation code is distributed without restrictions. The code for stable and efficient
computation of multinomial coefficients comes from Dave Barber. The code can be
download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is
distributed without conditions. The package also generates the integer partitions
of a positive, non-zero integer n. The C++ code for this is based on Python code
from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php.
The C++ code and Python code are distributed without conditions.
|
2023-06-16 |
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sickle
|
public |
A lightweight OAI client library for Python
|
2023-06-16 |
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svtyper
|
public |
Bayesian genotyper for structural variants
|
2023-06-16 |
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tophat
|
public |
A spliced read mapper for RNA-Seq
|
2023-06-16 |
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bcbio-nextgen-vm
|
public |
Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
|
2023-06-16 |
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ruby
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public |
No Summary
|
2023-06-16 |
