SAMSeq statistics

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SAMSeq specifications

Information


Unique identifier OMICS_01314
Name SAMSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SAMSeq

SAMSeq in pipeline

2014
PMCID: 3916258
PMID: 24516681
DOI: 10.1371/journal.pntd.0002678

[…] of coverage per million reads (dcpm) per sample . stage-specific over-expression and under-expression for each gene with at least 50% breadth of coverage across all of the tissues was tested using samseq (v4.0, released 2011 ). genes with less than 50% breadth of read coverage of the gene sequence across all samples were excluded from the analysis. this algorithm was chosen because (i) […]


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SAMSeq in publications

 (43)
PMCID: 5885026
PMID: 29615509
DOI: 10.1128/mBio.02401-17

[…] of reads mapping to these genomes are listed in ., the number of total reads mapped to each genome was used to determine the rpkm (reads per kilobase of transcript per million mapped reads). the samseq () package for the r platform was used to identify genes with significant changes between two samples. to identify genes with statistically different expressions between samples, we set […]

PMCID: 5817962
PMID: 29491871
DOI: 10.3389/fpls.2018.00108

[…] ). nevertheless, it seems that some tools are particularly appropriate. soneson and delorenzi () concluded that, for large sample sizes, the limma methods perform well, as does the non-parametric samseq tool. seyednasrollah et al. () concluded that limma and deseq methods are the safest choices with a small number of replicates, that edger gives very variable results, and that samseq suffers […]

PMCID: 5762563
PMID: 29348878
DOI: 10.18632/oncotarget.22878

[…] research., differential gene expression analysis has been widely used for identifying differentially expressed genes between conditions. the commonly used methods include edger [], limma [], samseq [] and deseq []. most studies only use one method to analyze gene expression patterns. soneson et al. compared the commonly used methods for differential expression analysis and found […]

PMCID: 5708087
PMID: 29187235
DOI: 10.1186/s13104-017-2950-9

[…] obtained were separated using the identified barcode sequences. reads were assigned annotation by comparing to genome and small rna databases., statistical analysis was done using the deseq 2 [] and samseq [] bioconductor packages for the r open source software. mirna were aggregated together into clusters, 1–43 mature mirna each, based on cistronic location in the genome, in order to reduce […]

PMCID: 5657123
PMID: 29070082
DOI: 10.1186/s13293-017-0153-7

[…] and to correct for multiple comparisons, we permuted each snp genotype 10,000 times and calculated a permutation-based fdr for the snp genotype*sex interaction term coefficient according to the samseq method [], which in turn is based on the fdr calculation described by storey and tibshirani []. the permuted p value and fdr cutoff was set to < 0.05., haploreg v.4.1 (1000 genomes phase 1, […]


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SAMSeq institution(s)
1Department of Statistics, Stanford University, Stanford, CA, USA

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