Sampbias – Sampling Bias in Species Distribution Records

Sampbias

:: DESCRIPTION

Sampbias is a method and tool to 1) visualize the distribution of occurrence records and species in any user-provided dataset, 2) quantify the biasing effect of geographic features related to human accessibility, such as proximity to cities, rivers or roads, and 3) create publication-level graphs of these biasing effects in space.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • R

:: DOWNLOAD

Sampbias

:: MORE INFORMATION

CodonO – Analysis of Synonymous Codon Usage Bias

CodonO

:: DESCRIPTION

CodonO is a new informatics method for measuring synonymous codon usage bias within and across genomes. CodonO measures Synonymous Codon Usage Order (SCUO) in a genomic scale by connecting directly GenBank genomic database. CodonO plots SCUO and GC compositions.

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 CodonO

:: MORE INFORMATION

Citation

Wan, X.-F., J. Zhou, and D. Xu. 2006.
CodonO: a new informatics method measuring synonymous codon usage bias.
International Journal of General Systems, 35: 109-125.

BIDCHIPS – Bias-Decomposition of ChIP-seq Signals

BIDCHIPS

:: DESCRIPTION

BIDCHIPS is a software for quantifying and Removing Biases in ChIP-Seq Signals

::DEVELOPER

Perkins Lab at the OHRI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  •  MatLab / R

:: DOWNLOAD

  BIDCHIPS

:: MORE INFORMATION

Citation

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.
Ramachandran P, Palidwor GA, Perkins TJ.
Epigenetics Chromatin. 2015 Sep 17;8:33. doi: 10.1186/s13072-015-0028-2.

SEQBIAS 1.16.0 – Estimation of Per-position Bias in High-throughput Sequencing data

SEQBIAS 1.16.0

:: DESCRIPTION

SEQBIAS implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

::DEVELOPER

Daniel C. Jones

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 SEQBIAS

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):921-8. doi: 10.1093/bioinformatics/bts055. Epub 2012 Jan 28.
A new approach to bias correction in RNA-Seq.
Jones DC, Ruzzo WL, Peng X, Katze MG.

BiasViz 2 – Protein Amino Acid Bias Analysis Applet

BiasViz 2

:: DESCRIPTION

BiasViz can be used to look at the composition of amino acids within a sliding window given a multiple sequence alignment. The window size and amino acid(s) of interest can be modified and the results are displayed in real time, allowing the user to tweak both of these parameters to their liking. The values can also be downloaded as a CSV file which allows further visualization in a separate program such as Microsoft Excel.

::DEVELOPER

Matthew R. Huska

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BiasViz

:: MORE INFORMATION

Citation

BiasViz: visualization of amino acid biased regions in protein alignments.
Huska MR, Buschmann H, Andrade-Navarro MA.
Bioinformatics. 2007 Nov 15;23(22):3093-4. Epub 2007 Oct 6.

Logopaint 1.0 – Exploring Visualisation of Bias in Regulatory DNA or RNA Element

Logopaint 1.0

:: DESCRIPTION

Logopaint is a software of exploring the visualisation of bias in regulatory DNA or RNA element, using information context and modified logos.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

Logopaint

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 Logopaint

:: MORE INFORMATION

Citation:

Bioinformatics. 2002 Apr;18(4):507-12.
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise.
Schreiber M1, Brown C.

CAST 1.0 – Compositional Bias Detection Algorithm

CAST 1.0

:: DESCRIPTION

CAST is a novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.

::DEVELOPER

Biophysics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy,Stavros J. Hamodrakas, Chris Sander, and Christos A. Ouzounis
CAST: an iterative algorithm for the complexity analysis of sequence tracts
Bioinformatics (2000), 16(10), 915-922.

HiCNorm – Removing Biases in Hi-C data via Poisson Regression

HiCNorm

:: DESCRIPTION

HiCNorm is a parametric model to remove systematic biases in the raw Hi-C contact maps. It relates chromatin interactions and systemic biases at the desired resolution level,resulting in a simple, yet accurate normalization procedure. Compared to the exiting Hi-C normalization method, our model has only a few parameters, is much easier to implement, can be interpreted intuitively, and achieves higher reproducibility in real Hi-C data

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 HiCNorm

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 1;28(23):3131-3. doi: 10.1093/bioinformatics/bts570. Epub 2012 Sep 27.
HiCNorm: removing biases in Hi-C data via Poisson regression.
Hu M1, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS.

glad – Gene Length Bias Detection in GWAS Datasets

glad

:: DESCRIPTION

glad is a software by randomly generating genomic intervals across the accessible genomic region to estimate the background distribution of P values at the gene level.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory, Vanderbilt University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

glad

:: MORE INFORMATION

Citation:

Int J Comput Biol Drug Des. 2010;3(4):297-310. doi: 10.1504/IJCBDD.2010.038394. Epub 2011 Feb 4.
Assessing gene length biases in gene set analysis of Genome-Wide Association Studies.
Jia P1, Tian J, Zhao Z.

MLbias 1.0 – Correct Machine Learning Bias

MLbias 1.0

:: DESCRIPTION

MLbias is an R package to correct for machine learning bias when many classifiers are compared and the best is selected

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MLbias

:: MORE INFORMATION

Citation:

Bias correction for selecting the minimal-error classifier from many machine learning models.
Ding Y, Tang S, Liao SG, Jia J, Oesterreich S, Lin Y, Tseng GC.
Bioinformatics. 2014 Aug 1. pii: btu520.