Selfish – Discovery of Differential Chromatin Interactions via a Self-Similarity Measure

Selfish

:: DESCRIPTION

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps. It uses self-similarity to model interactions in a robust way.

::DEVELOPER

Lonardi Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Matlab

:: DOWNLOAD

SELFISH

:: MORE INFORMATION

Citation

Ardakany AR, Ay F, Lonardi S.
Selfish: discovery of differential chromatin interactions via a self-similarity measure.
Bioinformatics. 2019 Jul 15;35(14):i145-i153. doi: 10.1093/bioinformatics/btz362. PMID: 31510653; PMCID: PMC6612869.

Chimericognizer – Optical Map based Chimeric Contigs Correction tool

Chimericognizer

:: DESCRIPTION

Chimericognizer is a novel and accurate chimeric contigs correction tool which can correct chimeric contigs and chimeric optical map molecules by each other.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Chimericognizer

:: MORE INFORMATION

Citation

Pan W, Lonardi S.
Accurate detection of chimeric contigs via Bionano optical maps.
Bioinformatics. 2019 May 15;35(10):1760-1762. doi: 10.1093/bioinformatics/bty850. PMID: 30295726.

PGA v2.0.4 – Post-GWAS Analysis

PGA v2.0.4

:: DESCRIPTION

PGA is a Java and Perl-based application with a command line interface for post-GWAS (Genome-wide association studies) analysis. The application incorporates gene regulatory information in producing a list of scored candidate disease genes from a set of GWAS-reported variants, where candidate scores indicate the strength of a gene’s relationship to the disease in question.

::DEVELOPER

ZDZ lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • Java
  • Perl

:: DOWNLOAD

PGA

:: MORE INFORMATION

Citation

Lin JR, Jaroslawicz D, Cai Y, Zhang Q, Wang Z, Zhang ZD.
PGA: post-GWAS analysis for disease gene identification.
Bioinformatics. 2018 May 15;34(10):1786-1788. doi: 10.1093/bioinformatics/btx845. PMID: 29300829; PMCID: PMC5946835.

Q5 – Classification of Complete Mass Spectra of a Complex Protein Mixture

Q5

:: DESCRIPTION

Q5 is a closed-form, exact solution to the problem of classification of complete mass spectra of a complex protein mixture. Q5 employs a probabilistic classification algorithm built upon a dimension-reduced linear discriminant analysis. Our solution is computationally efficient; it is non-iterative and computes the optimal linear discriminant using closed-form equations. The optimal discriminant is computed and verified for datasets of complete, complex SELDI spectra of human blood serum. Replicate experiments of different training/testing splits of each dataset are employed to verify robustness of the algorithm. The probabilistic classification method achieves excellent performance. We achieve sensitivity, specificity, and positive predictive values above 97% on three ovarian cancer datasets and one prostate cancer dataset. The Q5 method outperforms previous full-spectrum complex sample spectral classification techniques, and can provide clues as to the molecular identities of differentially-expressed proteins and peptides.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Matlab

:: DOWNLOAD

Q5

:: MORE INFORMATION

Citation

Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum
Ryan H. Lilien, Hany Farid and Bruce R. Donald
Journal of Computational Biology, 2003; 10(6): 925-946.

QRNAS – software tool for Refinement of Nucleic Acid structures

QRNAS

:: DESCRIPTION

QRNAS (Quick Refinement of Nucleic Acid Structures) is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues.

::DEVELOPER

Laboratory Of Bioinformatics And Protein Engineering

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

QRNAS

:: MORE INFORMATION

Citation

Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.
QRNAS: software tool for refinement of nucleic acid structures.
BMC Struct Biol. 2019 Mar 21;19(1):5. doi: 10.1186/s12900-019-0103-1. PMID: 30898165; PMCID: PMC6429776.

systemPipeR 1.27.27 – NGS Workflow and report Generation Environment

systemPipeR 1.27.27

:: DESCRIPTION

systemPipeR is an R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

systemPipeR

:: MORE INFORMATION

Citation

H Backman TW, Girke T.
systemPipeR: NGS workflow and report generation environment.
BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0. PMID: 27650223; PMCID: PMC5029110.

ISIF 1.1.3 – Performs in silico AFLP

ISIF 1.1.3

:: DESCRIPTION

ISIF (In SIlico Fingerprinting) is a free user-friendly software that performs in silico AFLP (can also be applied for DART or RAD).

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

ISIF

:: REQUIREMENTS

  • Windows with .net 2.0 

:: DOWNLOAD

 ISIF

:: MORE INFORMATION

Citation

Paris, M., Bonnes, B., Ficetola, G.F., Poncet, B.N., Despres, L. (2010)
Amplified fragment length homoplasy: in silico analysis for model and non-model species.
BMC Genomics 11:287.

ChemmineR 3.44.0 – Cheminformatics Toolkit for R

ChemmineR 3.44.0

:: DESCRIPTION

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 ChemmineR

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1733-4. doi: 10.1093/bioinformatics/btn307.
ChemmineR: a compound mining framework for R.
Cao Y, Charisi A, Cheng LC, Jiang T, Girke T.

gNOMO – Host and Microbiome analysis of non-model Organisms

gNOMO

:: DESCRIPTION

gNOMO is a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.

::DEVELOPER

gNOMO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

gNOMO

:: MORE INFORMATION

Citation

Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T.
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.
NAR Genom Bioinform. 2020 Aug 5;2(3):lqaa058. doi: 10.1093/nargab/lqaa058. Erratum in: NAR Genom Bioinform. 2020 Oct 09;2(4):lqaa083. PMID: 33575609; PMCID: PMC7671378.

GLnexus v1.4.1 – Scalable Joint Variant Calling

GLnexus v1.4.1

:: DESCRIPTION

GLnexus is an open-source cohort-calling method that uses the highly-accurate caller DeepVariant and scalable merging tool.

::DEVELOPER

Mike Lin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GLnexus

:: MORE INFORMATION

Citation

Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY.
Accurate, scalable cohort variant calls using DeepVariant and GLnexus.
Bioinformatics. 2021 Jan 5;36(24):5582–9. doi: 10.1093/bioinformatics/btaa1081. Epub ahead of print. PMID: 33399819; PMCID: PMC8023681.