Tag: Statistics

SCANSTAT – Scan Statistics for Disease Gene Association of a set of Contiguous SNPs

SCANSTAT

:: DESCRIPTION

SCANSTAT considers a number of marker loci in the genome. At each marker, genotypes are available for two types of observations

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SCANSTAT

:: MORE INFORMATION

Citation

Scan statistics to scan markers for susceptibility genes.
Hoh J, Ott J.
Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9615-7.

KCOSS 2021 – A K-mer Frequency Statistics Software

KCOSS 2021

:: DESCRIPTION

KCOSS is used to count the sequence files in FASTA format and save the statistical results as binary files to save space.

::DEVELOPER

KCOSS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

KCOSS

:: MORE INFORMATION

Citation:

Tang D, Li Y, Tan D, Fu J, Tang Y, Lin J, Zhao R, Du H, Zhao Z.
KCOSS: an ultra-fast k-mer counter for assembled genome analysis.
Bioinformatics. 2021 Nov 26:btab797. doi: 10.1093/bioinformatics/btab797. Epub ahead of print. PMID: 34849595.

KmerStream 1.1 – Computing kmer statistics for massive Genomics Datasets

KmerStream 1.1

:: DESCRIPTION

KmerStream is a streaming algorithm for estimating the number of distinct k-mers present in high throughput sequencing data.

::DEVELOPER

Pall Melsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • C++ COmpiler

:: DOWNLOAD

 KmerStream

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 28. pii: btu713.
KmerStream: Streaming algorithms for k-mer abundance estimation.
Melsted P, Halldórsson BV

Alfred v0.2.3 – BAM Alignment Statistics, Feature Counting and Annotation

Alfred v0.2.3

:: DESCRIPTION

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments

::DEVELOPER

Tobias Rausch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Alfred

:: MORE INFORMATION

Citation:

Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.
Bioinformatics. 2019 Jul 15;35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007. PMID: 30520945; PMCID: PMC6612896.

P.R.E.S.S. 2.0 – Exploring Residual-level Protein Structural Statistics

P.R.E.S.S. 2.0

:: DESCRIPTION

P.R.E.S.S. (Protein Residue-Level Structural Statistics) is an R-package developed to allow researchers to get access to and manipulate on a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles.

::DEVELOPER

PRESS Team

:: SCREENSHOTS

press

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 P.R.E.S.S.

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2012 Jun;10(3):1242007. doi: 10.1142/S0219720012420073.
P.R.E.S.S.–an R-package for exploring residual-level protein structural statistics.
Huang Y, Bonett S, Kloczkowski A, Jernigan R, Wu Z.

Pedgene 3.3 – Gene-level Statistics for Pedigree Data

Pedgene 3.3

:: DESCRIPTION

Pedgene offers an R package that performs gene-level kernel and burden association tests for genetic variants with disease status and continuous traits for pedigree data and unrelated subjects.

::DEVELOPER

Statistical Genetics and Genetic Epidemiology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 Pedgene

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Jul;37(5):409-18. doi: 10.1002/gepi.21727. Epub 2013 May 5.
Multiple genetic variant association testing by collapsing and kernel methods with pedigree or population structured data.
Schaid DJ1, McDonnell SK, Sinnwell JP, Thibodeau SN.

SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

PRINSEQ 0.20.4 – Preprocess and Generate Statistics about Sequence data

PRINSEQ 0.20.4

:: DESCRIPTION

PRINSEQ (PReprocessing and INformation of SEQuence data.) is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.

PRINSEQ Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 PRINSEQ

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Quality control and preprocessing of metagenomic datasets.
Bioinformatics 2011, 27:863-864.