Tag: Library

OBITools 1.2.13 – Scripts and Library for Sequence Analysis

OBITools 1.2.13

:: DESCRIPTION

OBITools is a set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.

::DEVELOPER

OBITools team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

 OBITools

:: MORE INFORMATION

Citation

OBITools: a Unix-inspired software package for DNA metabarcoding.
Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E.
Mol Ecol Resour. 2015 May 9. doi: 10.1111/1755-0998.12428.

Selene 0.4.8 – Library for deep-learning-based Sequence models

Selene 0.4.8

:: DESCRIPTION

Selene is a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Selene

:: MORE INFORMATION

Citation

Chen KM, Cofer EM, Zhou J, Troyanskaya OG.
Selene: a PyTorch-based deep learning library for sequence data.
Nat Methods. 2019 Apr;16(4):315-318. doi: 10.1038/s41592-019-0360-8. Epub 2019 Mar 28. PMID: 30923381; PMCID: PMC7148117.

Sleipnir 3.0 / COALESCE – Library for Computational Functional Genomics

Sleipnir 3.0 / COALESCE

:: DESCRIPTION

Sleipnir is a C++ library enabling efficient analysis, integration, mining, and machine learning over genomic data. This includes a particular focus on microarrays, since they make up the bulk of available data for many organisms, but Sleipnir can also integrate a wide variety of other data types, from pairwise physical interactions to sequence similarity or shared transcription factor binding sites.

COALESCE (Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction) can use large collections of genomic data and Bayesian integration to predict coregulated gene modules, the conditions of regulation, and the consensus binding motifs for regulation.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 Sleipnir

:: MORE INFORMATION

Citation

Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and Olga G. Troyanskaya
“The Sleipnir library for computational functional genomics”,
Bioinformatics. 2008 Jul 1;24(13):1559-61. Epub 2008 May 21.

Bioinformatics. 2009 Dec 15;25(24):3267-74. doi: 10.1093/bioinformatics/btp588.
Detailing regulatory networks through large scale data integration.
Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA.

Cytoscape.js 3.18.2 – Graph Theory Library for Visualisation and Analysis

Cytoscape.js 3.18.2

:: DESCRIPTION

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser.

::DEVELOPER

the Donnelly Centre at the University of Toronto.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • JavaScript

:: DOWNLOAD

 Cytoscape.js

:: MORE INFORMATION

Citation

Cytoscape.js: a graph theory library for visualisation and analysis.
Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD.
Bioinformatics. 2015 Sep 28. pii: btv557.

Bio++ 2.4.1 – C++ Libraries for Bioinformatics

Bio++ 2.4.1

:: DESCRIPTION

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bio++

:: MORE INFORMATION

Citation:

Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.
BMC Bioinformatics. 2006 Apr 4;7:188.

BIU 2.3.7 – Bioinformatic Utility Library

BIU 2.3.7

:: DESCRIPTION

BIU (Bioinformatic Utility Library) is a C++ programming library provides a classes and functions often used in the bioinformatics context. It collects data structures and class hierarchies for biomolecule modelling and general usefull functionalities as program parameter parsing, string conversions, etc.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIU

:: MORE INFORMATION

pyDNase 0.2.4 – a Library for Analyzing DNase-seq data

pyDNase 0.2.4

:: DESCRIPTION

Wellington is a novel method for the accurate identification of digital genomic footprints from DNase-seq data.
pyDNase is an open-source software package which implements the Wellington algorithm to interface with DNase-seq data and expedite analyses.

::DEVELOPER

Dr Sascha Ott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 pyDNase

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Nov;41(21):e201. doi: 10.1093/nar/gkt850. Epub 2013 Sep 25.
Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.
Piper J1, Elze MC, Cauchy P, Cockerill PN, Bonifer C, Ott S.

rlsim 1.4 – Simulating RNA-seq library Preparation with Parameter Estimation

rlsim 1.4

:: DESCRIPTION

The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Biopython

:: DOWNLOAD

  rlsim

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham and Nick Goldman (2013):
rlsim – a package for simulating RNA-seq library preparation with parameter estimation.
http://bit.ly/rlsim-doc

PLL 1.0.2 / libpll-2 0.3.2 – Phylogenetic Likelihood Library

PLL 1.0.2 / libpll-2 0.3.2

:: DESCRIPTION

PLL is a highly optimized and parallized library for rapid prototyping and development of likelihood based phylogenetic inference codes.

libpll-2 is the new official fork of libpll

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C COmpiler

:: DOWNLOAD

 PLL, libpll-2

:: MORE INFORMATION

Citation

The phylogenetic likelihood library.
Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A.
Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084.

SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1 – Systems Biology Library for R

SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1

:: DESCRIPTION

The package SyBiL is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks.

The R-package sybilSBML provides support for models written in SBML format.

The R-package sybilFCF computes extreme pathways and coupled reaction sets.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SyBiL / sybilSBML  / sybilFCF

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Nov 13;7:125. doi: 10.1186/1752-0509-7-125.
Sybil–efficient constraint-based modelling in R.
Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ.