version 1.0-2

Author: devSJR

CHANGELOG

@@ -1,3 +1,20 @@
+Changes from Version 0.0.8-13 to 1.0 [Marach 2021]
+* Update maintainer email
+* Transition of Rnw to Rmd [WIP]
+* the first stable version
+
+Changes from Version 0.0.8-11 to 0.0.8-12 [February 02 2018]
+* Improved plot of humanrater
+* Fixed function poc in amptester
+* Improved documentation for amptester
+* adopted the fairly new CRAN requirements
+* removed natbib.sty from vignettes
+* some improvements to grammar and spelling
+
+Changes from Version 0.0.8-10 to 0.0.8-11 [April 31 2015]
+* further CRAN changes, VideoScan -> 'VideoScan', HCU -> 'HCU'
+* some further test of validity for the th.cyc function
+
 Changes from Version 0.0.8-9 to 0.0.8-10 [April 8 2015]
 * further CRAN changes
 

DESCRIPTION

@@ -1,31 +1,42 @@
 Package: chipPCR
 Type: Package
 Title: Toolkit of Helper Functions to Pre-Process Amplification Data
-Version: 0.0.8-10
+Version: 1.0-2
 LazyData: true
-Date: 2015-04-08
+Date: 2021-03-02
 Authors@R: c(
     person("Stefan", "Roediger", 
-	   email = "[email protected]",
+	   email = "[email protected]",
+	   comment = c(ORCID = "0000-0002-1441-6512"),
       role = c("cre", "aut")),
     person("Michal", "Burdukiewicz", 
-      email = "[email protected]", role = "aut"),
+      email = "[email protected]", 
+      comment = c(ORCID = "0000-0001-8926-582X"),
+      role = "aut"),
     person("Konstantin A.", "Blagodatskikh",
-      email = "[email protected]", role = "ctb"))
-Description: A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. 
+      email = "[email protected]", role = "ctb"),
+    person("Andrej-Nikolai", "Spiess", 
+      email = "[email protected]", 
+      role = c("ctb"),
+      comment = c(ORCID = "0000-0002-9630-4724")))
+Description: A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>. 
 License: GPL-3
-URL: https://github.com/michbur/chipPCR
-BugReports: https://github.com/michbur/chipPCR/issues
+URL: https://github.com/PCRuniversum/chipPCR
+BugReports: https://github.com/PCRuniversum/chipPCR/issues
 Depends: R (>= 3.0.0), methods
-Suggests: drc, knitr, markdown, MBmca (>= 0.0.3-4), qpcR, RDML, xtable
-VignetteBuilder: knitr
+Suggests: drc, knitr, markdown, qpcR, RDML, rmarkdown, spelling,
+        testthat, tinytex, xtable
+VignetteBuilder: knitr, rmarkdown
 Imports: lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase,
         shiny, signal
-Packaged: 2015-04-09 18:11:32 UTC; tux
 NeedsCompilation: no
 Repository: CRAN
-Date/Publication: 2015-04-10 01:10:56
-Author: Stefan Roediger [cre, aut],
-  Michal Burdukiewicz [aut],
-  Konstantin A. Blagodatskikh [ctb]
-Maintainer: Stefan Roediger <[email protected]>
+Language: en-US
+RoxygenNote: 7.1.1
+Packaged: 2021-03-04 14:36:42 UTC; tux
+Author: Stefan Roediger [cre, aut] (<https://orcid.org/0000-0002-1441-6512>),
+  Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>),
+  Konstantin A. Blagodatskikh [ctb],
+  Andrej-Nikolai Spiess [ctb] (<https://orcid.org/0000-0002-9630-4724>)
+Maintainer: Stefan Roediger <[email protected]>
+Date/Publication: 2021-03-05 07:50:03 UTC

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NAMESPACE

@@ -2,14 +2,23 @@ importFrom(lmtest, bptest)
 importFrom(MASS, rlm)
 import("methods")
 importFrom(outliers, rm.outlier)
-importFrom(parallel, parLapplyLB)
 importFrom(ptw, whit1, whit2)
 importFrom(quantreg, rq)
 importFrom(Rfit, rfit)
 importFrom(robustbase, lmrob)
 importFrom(robustbase, mc)
 importFrom(shiny, runApp)
 importFrom(signal, sgolayfilt)
+importFrom(graphics, abline, arrows, axis, layout, legend,
+           lines, matplot, mtext, par, points, polygon,
+           rect, rug, text)
+importFrom(grDevices, adjustcolor)
+importFrom(stats, coef, confint, cor, cor.test, lm, mad, median, na.omit,
+           predict, predict.lm, qnorm, quantile, rnorm,
+           rstudent, sd, shapiro.test, smooth.spline,
+           wilcox.test)
+importFrom(utils, head, tail)
+
 
 exportClasses(
     "amptest",
@@ -44,4 +53,4 @@ export(
 	"rounder",
 	"smoother",
 	"th.cyc"
-)
+)