BIC-seq statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left CNV detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

BIC-seq specifications

Information


Unique identifier OMICS_03362
Name BIC-seq
Alternative name BIC-seq2
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BAM
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Ruibin Xi <>

Publications for BIC-seq

BIC-seq in publications

 (18)
PMCID: 5932867
PMID: 29720102
DOI: 10.1186/s12864-018-4709-7

[…] parameters. two methods were used to evaluate copy number variation (cnv) in each of p. ramorum isolates. the first method detects cnvs from bwa aligned reads using a read-depth algorithm called bic-seq []. to minimize experimental noise, the genome sequence isolate nd886 (cdfa1418886), an euploid isolate from camellia found in a nursery, and pr-1556, an euploid isolate from california bay, […]

PMCID: 5865353
PMID: 29566644
DOI: 10.1186/s12885-018-4199-7

[…] default parameters. fusions were called by self-developed scripts with at least 5 pairs of reads spanned over the breakpoints between two partner genes. the cnvs of tumor tissues were calculated by bic-seq2 [] with default parameters, and the cnvs of ctdna samples were called by a method reported by jacob j. chabon et al. []. all mutations were manually reviewed using igv [] […]

PMCID: 5668369
PMID: 29097733
DOI: 10.1038/s41598-017-14962-0

[…] escribed in research by bellos e et al.. we split the whole genome into bins with 500kb length and count the read depth (rd) in each bin, followed by gc normalization method described by yu z et al.. bic-seq was used for segmentation of off-target sequencing data., the experimental data are presented as the mean ± sem and were analyzed with the two-tailed student’s t test. the threshold of p <  […]

PMCID: 5590190
PMID: 28882180
DOI: 10.1186/s13046-017-0591-4

[…] or <0.1, maf threshold <1% while maf < 0.5% at hotspots), with an empirically increased requirement at repeats., a statistically rigorous and computationally efficient algorithm called bic-seq was used for detecting cnvs. in this algorithm, a poisson or other parametric models are not assumed on the read distribution as is done in other currently available methods, and it is thus […]

PMCID: 5343482
PMID: 28262751
DOI: 10.1038/ncomms14648

[…] least two of the six samples (two replicates of three conditions each) were retained to remove any non-reproducible calls., the genome was segmented based on poliii enrichment in wild-type using the bic-seq command line tool mbicseq with option ‘l 1', and providing polii and input read counts in 100 bp bins. segments with average log2-enrichment greater than 0.1 were selected as transcribed […]


To access a full list of publications, you will need to upgrade to our premium service.

BIC-seq institution(s)
School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Quantitative Biology, Peking University, Beijing, China; Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea
BIC-seq funding source(s)
Supported by National Institutes of Health (NIH) [R01EY024230]; Ludwig Cancer Center; National Natural Science Foundation of China [11471022 and 71532001]; National Key Basic Research Program of China [2015CB856000]; Recruitment Program of Global Youth Experts of China.

BIC-seq reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BIC-seq