:: 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
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm.
::DEVELOPER
JRG 4: Bioinformatics Research Group Bioinformatics (NG4), Robert Koch-Institut
: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Analyzing genome coverage profiles with applications to quality control in metagenomics
Martin S. Lindner, Maximilian Kollock, Franziska Zickmann and Bernhard Y. Renard,
Bioinformatics (2013) 29 (10): 1260-1267.
:: DESCRIPTION
InVEx (Introns Vs Exons) is a permutation-based method for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer genomics studies, with particular relevance to high mutation rate cancers. Mutations are permuted on a per-patient, per-trinucleotide-context basis across the exons, introns and UTRs of a gene, generating a null model of the distribution of mutations to which the observed distribution can be compared to determine statistical significance. Significant genes are of interest, as their somatic mutation is likely to be important in the formation of the cancer being studied. The method can operate on whole exome as well as whole genome sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hodis and Watson et al
A Landscape of Driver Mutations in Melanoma
Cell, Volume 150, Issue 2, 251-263, 20 July 2012
:: DESCRIPTION
shulen is a program for computing the null-distribution of shortest unique substring lengths in DNA sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bernhard Haubold, Nora Pierstorff, Friedrich Möller and Thomas Wiehe
Genome comparison without alignment using shortest unique substrings
BMC Bioinformatics 2005, 6:123
:: DESCRIPTION
GMM (Gaussian Mixture Model) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).
::DEVELOPER
Computational Biology Group ,Department of Medical Genetics, University of Lausanne
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MM-DIST is a computer program that calculates probability distributions for how many loci individuals in a population will differ by. For example, the graph below shows the probability of two individuals differing (mismatching) by 0 to 10 loci for unrelated individuals (solid line) and full siblings (dashed line) in a population of bighorn sheep.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalinowski ST, M Sawaya, ML Taper (2006)
Individual identification and distributions of genotypic differences.
Journal of Wildlife Management 70:148-150.
