CNVineta 1.0-1 – Data mining tool for large case-control copy number variation data sets

CNVineta 1.0-1

:: DESCRIPTION

CNVineta is a flexible data mining tool for the analysis of copy number variations (CNVs) in large case-control SNP array data sets. The tool is available as an R statistical package. CNVineta offers a flexible and fast access to CNVs by a quick graphical overview in large case-control datasets. In addition, CNVineta provides rapid access to the log2 of raw data ratios (LRR) and B-allele frequencies (BAF) of specific or all samples, thereby allowing for a fast verification of the underlying raw data. CNVineta is also equipped with analysis methods for genome-wide screening for associated rare as well as common CNVs. Hence, CNVineta is a unique data mining tool to rapidly explore CNVs in large case-control data sets.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 CNVineta

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2208-9. Epub 2010 Jul 6.
CNVineta: a data mining tool for large case-control copy number variation datasets.
Wittig M, Helbig I, Schreiber S, Franke A.

varLD 1.0 – Comparison of Variation in Linkage Disequilibrium between Population

varLD 1.0

:: DESCRIPTION

varLD can be used to perform inter-population comparison of regional patterns of linkage disequilibrium (LD), and quantifies which genomic regions carry dissimilar patterns of LD across the populations compared.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsXR package
  • Java

:: DOWNLOAD

  varLD

:: MORE INFORMATION

Citation:

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations.
Ong RT, Teo YY.
Bioinformatics. 2010 May 1;26(9):1269-70. doi: 10.1093/bioinformatics/btq125. Epub 2010 Mar 22.

HiNT v2.2.7 – Hi-C for Copy Number Variation and Translocation Detection

HiNT v2.2.7

:: DESCRIPTION

HiNT is a computational method to detect CNVs and Translocations from Hi-C data.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl
  • R package
  • Python

:: DOWNLOAD

HiNT

:: MORE INFORMATION

Citation

Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ.
HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.
Genome Biol. 2020 Mar 23;21(1):73. doi: 10.1186/s13059-020-01986-5. PMID: 32293513; PMCID: PMC7087379.

RUbioSeq 3.8.1 – Parallelized pipelines to automate Exome Variation and Bisulfite-seq Analyses

RUbioSeq 3.8.1

:: DESCRIPTION

RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically.

::DEVELOPER

Miriam Rubio-Camarillo at Spanish National Cancer Research Centre (CNIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java
  • Samtools
  • Fastqc

:: DOWNLOAD

 RUbioSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1687-9. doi: 10.1093/bioinformatics/btt203. Epub 2013 Apr 28.
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG.

FEATnotator 1.1.3 – Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments

FEATnotator 1.1.3

:: DESCRIPTION

FEATnotator is a light weight, fast and easy to use, open source software program that annotates different kinds of next generation analysis data based on known reference genome annotation information.

::DEVELOPER

FEATnotator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • R

:: DOWNLOAD

 FEATnotator

:: MORE INFORMATION

Citation:

FEATnotator: A Tool for Integrated Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments.
Podicheti R, Mockaitis K.
Methods. 2015 Apr 28. pii: S1046-2023(15)00175-9. doi: 10.1016/j.ymeth.2015.04.028

SHiAT 1.1 – Generates Plots of Variation along Sequence Alignment

SHiAT 1.1

:: DESCRIPTION

SHiAT (Shannon Heterogeneity in Alignments Tool) provides an intuitive graphical interface for the simultaneous calculation of three measures of sitewise variation in DNA or RNA alignments. The Shannon Information index, Hamming distance and (1-consensus frequency) are all calculated and displayed in a series of graphical plots. Multiple alignments may be imported and compared, and a data view panel allows easy copy-and-pasting into external applications.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

SHiAT

:: MORE INFORMATION

TrioCNV 0.1.2 – Joint Detection of Copy Number Variations in Parent-offspring Trios

TrioCNV 0.1.2

:: DESCRIPTION

TrioCNV is a tool designed to jointly detecting CNVs from WGS data in parent-offspring trios.

::DEVELOPER

yzhuangliu@gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R
  • JRE

:: DOWNLOAD

 TrioCNV

:: MORE INFORMATION

Citation

Joint detection of copy number variations in parent-offspring trios.
Liu Y, Liu J, Lu J, Peng J, Juan L, Zhu X, Li B, Wang Y.
Bioinformatics. 2015 Dec 7. pii: btv707.

WebSTR – Population-wide database of short Tandem Repeat Variation in humans

WebSTR

:: DESCRIPTION

WebSTR is a web application for browsing a variety of STR datasets. It is based off of the popular ExAC browser.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

 

PyLOH 1.4.3 – Discovering Copy Number Variations in Cancer Genomes

PyLOH 1.4.3

:: DESCRIPTION

PyLOH is a tool for discovering copy number variations in cancer genomes

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python

:: DOWNLOAD

  PyLOH

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 21.
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.
Li Y1, Xie X.