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Package: cTRAP | ||
Title: Identification of potential transcriptome perturbations | ||
Version: 0.99.12 | ||
Authors@R: c(person("Nuno", "Agostinho", | ||
email="[email protected]", role=c("aut", "cre")), | ||
person("Bernardo", "de Almeida", role="aut"), | ||
person(c("Nuno", "Luís"), "Barbosa-Morais", role=c("aut", "led"))) | ||
Title: Identification of candidate causal perturbations from differential gene | ||
expression data | ||
Version: 1.0.1 | ||
Authors@R: c( | ||
person(c("Bernardo", "P."), "de Almeida", role="aut"), | ||
person("Nuno", "Saraiva-Agostinho", | ||
email="[email protected]", role=c("aut", "cre")), | ||
person(c("Nuno", "L."), "Barbosa-Morais", role=c("aut", "led"))) | ||
Description: Compare differential gene expression results with those from known | ||
cellular perturbations (such as gene knock-down, overexpression or small | ||
molecules) derived from the Connectivity Map. Such analyses allow not only | ||
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@@ -21,15 +23,15 @@ URL: https://github.com/nuno-agostinho/cTRAP | |
BugReports: https://github.com/nuno-agostinho/cTRAP/issues | ||
Suggests: testthat, | ||
knitr, | ||
covr | ||
covr, | ||
biomaRt | ||
RoxygenNote: 6.1.0 | ||
Imports: data.table, | ||
limma, | ||
stats, | ||
fgsea, | ||
pbapply, | ||
plyr, | ||
biomaRt, | ||
cowplot, | ||
ggplot2, | ||
rhdf5, | ||
|
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# 0.0.0.9000 | ||
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* Added a `NEWS.md` file to track changes to the package. | ||
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# 1.0.1 (2 November, 2018) | ||
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* Update title, author names, version and README | ||
* Remove biomaRt dependency | ||
* By default, `getL1000conditions` now shows CMap perturbation types except for | ||
controls | ||
* Compare against CMap perturbations (`compareAgainstL1000` function): | ||
- Remove "_t" from resulting column names (as the t-statistic may or may not | ||
be used) | ||
- Select p-value adjustment method when performing correlation analyses | ||
(Benjamini-Hochberg is set by default) | ||
* Documentation: | ||
- Fix obsolete function calls in function documentation | ||
- Hide non-exported functions from reference PDF manual |
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