JointSLM protocols

View JointSLM computational protocol

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Popular tool citations

chevron_left CNV detection Deletion detection Duplication detection Somatic CNA detection chevron_right
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Associated diseases

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JointSLM specifications

Information


Unique identifier OMICS_00346
Name JointSLM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Alberto Magi <>

Additional information


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Publication for JointSLM

JointSLM in pipeline

2017
PMCID: 5267451
PMID: 28122487
DOI: 10.1186/s12711-017-0286-5

[…] to small and medium-sized sv because of the limit set on insert size while snp chip data only capture large sv. one potential better comparison would be to use an rd method such as cnvnator [] and jointslm [] that target large sv events and then to compare them with sv from snp chip data., another consideration is that sv detection from wgs data relies on differences with a reference genome, […]


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JointSLM in publications

 (4)
PMCID: 4570720
PMID: 26374103
DOI: 10.1186/s40246-015-0044-0

[…] samples as input and identify the (merged) segments which appear more frequently across the population than expected by chance. only a few rcna methods have been developed for ngs data, including jointslm [] and cn.mops []. they conduct copy number analyses based on read counts of segments of multiple tumor samples and usually are applied for cnv detection. on the other hand, many rcna […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] length., a considerable number of methods for the detection of cnv in whole-genome sequencing (wgs) data have been reported in the literature, including cnvnator, cnanorm, cnaseg, rsw-seq, cn.mops, jointslm, readdepth, and bic-seq (ivakhno et al., ; kim et al., ; abyzov et al., ; magi et al., ; miller et al., ; xi et al., ; gusnanto et al., ; klambauer et al., ). recently, pscc (li et al., ) […]

PMCID: 4194081
PMID: 25342930
DOI: 10.1186/1472-6815-14-9

[…] methods on cnv detections from ngs data are designed for examining cnvs on the whole genome or whole exome scale, with specific mathematical models applied in the algorithms []. for example, jointslm and exocnvtest are designed to detect common cnvs shared among many samples. conifer and xhmm are made to detect rare cnvs using population data. in our approach, we used the average […]

PMCID: 3604020
PMID: 23527109
DOI: 10.1371/journal.pone.0059128

[…] signature based methods with the single signature based methods can be found in . it was already shown that modeling across samples can improve the performance considerably , , and therefore jointslm and cn.mops were not compared in this paper for fairness. since they are developed for the purpose of population studies, multiple samples (recommended at least 10 and 6 samples […]


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JointSLM institution(s)
Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence, Italy
JointSLM funding source(s)
Supported by the project ‘‘Gene expression profile and therapeutic implication in gastric cancer. From the clinical overview to the translational research’’ of the Istituto Toscano Tumori (ITT).

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