=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== r-bioc-destiny-3.4.0/inst/CITATION-2- if ('Authors' %in% names(meta)) meta$Authors r-bioc-destiny-3.4.0/inst/CITATION:3: else eval(parse(text = meta$`Authors@R`)) r-bioc-destiny-3.4.0/inst/CITATION-4-) ############################################## r-bioc-destiny-3.4.0/inst/doc/Diffusion-Maps.ipynb-210- "\n", r-bioc-destiny-3.4.0/inst/doc/Diffusion-Maps.ipynb:211: "The object internally stores an expression matrix of features × samples, retrievable using `exprs(ct)`, and an annotation `data.frame` of samples × annotations as `phenoData(ct)`. Annotations can be accessed directly via `ct$column` and `ct[['column']]`. Note that the expression matrix is transposed compared to the usual samples × features `data.frame`.\n", r-bioc-destiny-3.4.0/inst/doc/Diffusion-Maps.ipynb-212- "\n", ############################################## r-bioc-destiny-3.4.0/inst/doc/Global-Sigma.ipynb-21- "\n", r-bioc-destiny-3.4.0/inst/doc/Global-Sigma.ipynb:22: "The other important parameter for `DiffusionMap` is the Gaussian kernel width `sigma` ($\\sigma$) that determines the transition probability between data points. The default call of **destiny** – `DiffusionMap(data)` aka `DiffusionMap(data, 'local')`) – uses a local `sigma` per cell, derived from a local density estimate around each cell.\n", r-bioc-destiny-3.4.0/inst/doc/Global-Sigma.ipynb-23- "\n", ############################################## r-bioc-destiny-3.4.0/inst/doc/tidyverse.ipynb-202- "source": [ r-bioc-destiny-3.4.0/inst/doc/tidyverse.ipynb:203: "`names(dm)` shows what names can be used in `dm$<name>`, `as.data.frame(dm)$<name>`, or `ggplot(dm, aes(<name>))`:" r-bioc-destiny-3.4.0/inst/doc/tidyverse.ipynb-204- ] ############################################## r-bioc-destiny-3.4.0/vignettes/Diffusion-Maps.ipynb-210- "\n", r-bioc-destiny-3.4.0/vignettes/Diffusion-Maps.ipynb:211: "The object internally stores an expression matrix of features × samples, retrievable using `exprs(ct)`, and an annotation `data.frame` of samples × annotations as `phenoData(ct)`. Annotations can be accessed directly via `ct$column` and `ct[['column']]`. Note that the expression matrix is transposed compared to the usual samples × features `data.frame`.\n", r-bioc-destiny-3.4.0/vignettes/Diffusion-Maps.ipynb-212- "\n", ############################################## r-bioc-destiny-3.4.0/vignettes/Global-Sigma.ipynb-21- "\n", r-bioc-destiny-3.4.0/vignettes/Global-Sigma.ipynb:22: "The other important parameter for `DiffusionMap` is the Gaussian kernel width `sigma` ($\\sigma$) that determines the transition probability between data points. The default call of **destiny** – `DiffusionMap(data)` aka `DiffusionMap(data, 'local')`) – uses a local `sigma` per cell, derived from a local density estimate around each cell.\n", r-bioc-destiny-3.4.0/vignettes/Global-Sigma.ipynb-23- "\n", ############################################## r-bioc-destiny-3.4.0/vignettes/tidyverse.ipynb-202- "source": [ r-bioc-destiny-3.4.0/vignettes/tidyverse.ipynb:203: "`names(dm)` shows what names can be used in `dm$<name>`, `as.data.frame(dm)$<name>`, or `ggplot(dm, aes(<name>))`:" r-bioc-destiny-3.4.0/vignettes/tidyverse.ipynb-204- ] ############################################## r-bioc-destiny-3.4.0/debian/tests/run-unit-test-5-if [ "$AUTOPKGTEST_TMP" = "" ] ; then r-bioc-destiny-3.4.0/debian/tests/run-unit-test:6: AUTOPKGTEST_TMP=`mktemp -d /tmp/${debname}-test.XXXXXX` r-bioc-destiny-3.4.0/debian/tests/run-unit-test-7- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM