BSPAT statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool BSPAT
info

Tool usage distribution map

info info

Associated diseases

info

Popular tool citations

chevron_left Quality control Read alignment Methylation scoring chevron_right
Want to access the full stats & trends on this tool?

BSPAT specifications

Information


Unique identifier OMICS_07897
Name BSPAT
Alternative name Bisulfite Sequencing Pattern Analysis Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Tomcat, Bismark, Perl, Bowtie
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Jing Li

Information


Unique identifier OMICS_07897
Name BSPAT
Alternative name Bisulfite Sequencing Pattern Analysis Tool
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jing Li

Publication for Bisulfite Sequencing Pattern Analysis Tool

BSPAT citations

 (6)
library_books

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13 gene panel

2017
Clin Epigenetics
PMCID: 5558660
PMID: 28814981
DOI: 10.1186/s13148-017-0386-7

[…] methylation pattern independently of the ratio, while all six HGSIL enrolled in this study showed an irregular methylation pattern among various CpGs as exemplified in Fig. for case 31.Fig. 2 After BSPAT data processing [] (see “” for the bioinformatic pipeline), a ROC analysis for each CpG of all 18 genes evaluating differences between OSCC and normal healthy donors is performed and summarized […]

library_books

Profiling genome wide DNA methylation

2016
PMCID: 4926291
PMID: 27358654
DOI: 10.1186/s13072-016-0075-3

[…] er out sites with coverage, calculate the average methylation level and generate informative plots. Table  lists 5 post-alignment analysis tools, and each of these tools has specific functions, e.g., BSPAT can detect allele-specific methylation [], SAAP-RRBS can extract the annotation of each C [] and MethGo can convert context methylation levels into average and genome-wide plots, as well as extr […]

library_books

Spatial analysis of gender variation in the prevalence of hypertension among the middle aged and elderly population in Zhejiang Province, China

2016
BMC Public Health
PMCID: 4882773
PMID: 27230660
DOI: 10.1186/s12889-016-3121-y

[…] f our dataset.Convolution prior was adopted for φ[i] and ν[j,i] [], denoting they both may be decomposed into the sum of unstructured (e.g. ush, ssh) and spatial structured random effects (e.g. bind, bspat):7φi=ushi+sshi8υji=bindji+bspatjiThen ush and bind were all assigned Normal prior with their mean zero and α0[j] respectively, while that of ssh, bspat and β[i] were Conditional Autoregressive ( […]

library_books

Determinants of Low Birth Weight in Malawi: Bayesian Geo Additive Modelling

2015
PLoS One
PMCID: 4482619
PMID: 26114866
DOI: 10.1371/journal.pone.0130057

[…] y: ε jm = 2ε j,m-1+ε j,m-2+u j.m where m = 3,4,…,d and uj.m~N(0,τj2) are random errors. The spatial effect was modelled by the tensor product of two dimensional p-spline defined as fspat(x1,x2)=∑ik∑jkBspat, ijB1i(x1)B2j(x2)(4) where (x 1,x 2) refers to the coordinates of the location of the data point, latitude and longitude, or location centroids based on the map. Note that f spat(x 1,x 2) repres […]

library_books

Bayesian random effects modelling with application to childhood anaemia in Malawi

2015
BMC Public Health
PMCID: 4358301
PMID: 25885648
DOI: 10.1186/s12889-015-1494-y

[…] εj,m = 2εj,m − 1 + εj,m − 2 + uj,m where m = 3, 4, …, d and uj.m~N0,τj2 are random errors. The spatial effect was modelled by the tensor product of two dimensional spline defined as2fspatx1,x2=∑ik∑jkBspat,ijB1ix1B2jx2where (x1, x2) refers to the coordinates of the location of the data point, latitude and longitude, or location centroids based on the map. The prior for Bspat, ij = (Bspat,11, Bspat […]

library_books

Space time confounding adjusted determinants of child HIV/TB mortality for large zero inflated data in rural South Africa

2011
PMCID: 4250009
PMID: 22748220
DOI: 10.1016/j.sste.2011.07.001

[…] graphic (spatial) variability known as the sill and ρ^=maxij‖si-sj‖/0.001 is the empirically estimated rate of spatial correlation decay (). Multivariate Gaussian random field (GRF) priors fspat(s)=p(βspat|σspat2)∝|∑|-12exp-1σspat2(βspat)′∑-1βspat, where βspat is the vector of household specific structured spatial coefficients, whereas the non-structured utilize the independent and identically dis […]


Want to access the full list of citations?
BSPAT institution(s)
Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA

BSPAT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BSPAT