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Scotty specifications

Information


Unique identifier OMICS_01315
Name Scotty
Interface Web user interface
Restrictions to use None
Input data A file containing the number of reads per gene for pilot data.
Input format TSV
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Gabor Marth <>

Publication for Scotty

Scotty in publications

 (5)
PMCID: 5810475
PMID: 28614673
DOI: 10.1080/21505594.2017.1342910

[…] is available in data set s1. to determine if the number of reads mapped to p. destructans transcripts provided sufficient statistical power to detect differential expression of these genes, we used scotty to analyze the expected counts generated by rsem. we determined that 65% of p. destructans genes expressed at a minimum of 4-fold change could be detected with a p-value cutoff of 0.05. […]

PMCID: 5403975
PMID: 28462379
DOI: 10.1016/j.jcmgh.2016.12.008

[…] foster city, ca). mix 1 was added to rna from fed intestine and mix 2 was added to rna from unfed intestine. libraries initially were sequenced to 10 million reads for power analysis via the scotty algorithm. based on the results of the power analysis, libraries then underwent deep sequencing to 40 million base pairs. sequences were assayed for quality using fastqc, and adapter sequences […]

PMCID: 4839710
PMID: 27100792
DOI: 10.1371/journal.pone.0153782

[…] (tmm) normalized fpkm matrix. quantification results of htseq and rsem were further normalized by using cqn []. roc curves were calculated using proc package []. power analysis was performed with scotty [] and r package rnaseqpower []., the spike-ins plots were done using matlab, partek and r. for spike-ins quantification plots an offset of 10e-3 was added to fpkm values before log2 […]

PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] power for lowly expressed genes [, ], and for any given sample there exists a level of sequencing at which power improvement is best achieved by increasing the number of replicates []. tools such as scotty are available to calculate the best trade-off between sequencing depth and replicate number given some budgetary constraints [].table 1example of calculations for the probability of detecting […]

PMCID: 4596860
PMID: 26445145
DOI: 10.1371/journal.pone.0139549

[…] on rna-seq analysis is provided in ., abbreviations: fat line (fl), lean line (ll), and million (m)., a power analysis was performed on this rna-seq dataset using the web-based software program “scotty” (http://euler.bc.edu/marthlab/scotty/scotty.php) []. this analysis demonstrates that our sample size of four birds/genotype (n = 4), sequenced across three depths [38.5 million mapped reads […]


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Scotty institution(s)
Department of Biology, Boston College, Chestnut Hill, MA, USA
Scotty funding source(s)
Supported by R01 HG004719 from NHGRI.

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