Commit 2a0b5d4a authored by Holger Brandl's avatar Holger Brandl

cosmetics; updated kotlin dependencies

parent ee1cdecc
......@@ -64,8 +64,15 @@ In as.data.frame(x, row.names = NULL, optional = optional, ...) :
```
How to tag it for a project
---------------------------
How to report used version for a project?
-----------------------------------------
```bash
(cd ${NGS_TOOLS} && git diff --exit-code && git rev-parse HEAD) > ${PRJ_DATA}/.used_ngs_tools
```
How to tag it for a project (Deprecated)
----------------------------------------
```bash
# ensure there are no pending changes
......@@ -83,6 +90,8 @@ git push --tags
```
How to create a new version tag
-------------------------------
......
......@@ -245,6 +245,7 @@ rld = rlogTransformation(dds)
#varstab = vst(dds) ## vst is supposed to be much 1k x faster
#plotPCA(rld, intgroup = "sample")
# plotPCA(rld, intgroup = "batch")
plotPCA(rld, intgroup = contrastAttribute)
......@@ -359,9 +360,6 @@ deResults %>% ggplot(aes(s1_over_s2_logfc)) +
ggtitle("sample1 over sampl2 logFC ")
session::save.session(".featcounts_deseq_mf.debug.dat");
# session::restore.session(".featcounts_deseq_mf.debug.dat")
########################################################################################################################
#' ## Significnce of differential binding
......@@ -792,5 +790,6 @@ mat <- assay(rld) %>%
mat <- mat - rowMeans(mat)
pheatmap(mat, annotation_col = column2rownames(exDesign, "replicate") %>% select(- col_index))
session::save.session(".featcounts_deseq_mf.dat");
# session::restore.session(".featcounts_deseq_mf.dat");
......@@ -7,7 +7,7 @@
<version>1.0-SNAPSHOT</version>
<properties>
<kotlin.version>1.0.5-2</kotlin.version>
<kotlin.version>1.1.2</kotlin.version>
</properties>
......@@ -20,8 +20,8 @@
<dependency>
<groupId>de.mpicbg.scicomp</groupId>
<artifactId>joblist</artifactId>
<version>0.6</version>
<artifactId>joblist-kotlin</artifactId>
<version>1.1</version>
</dependency>
<dependency>
......@@ -43,7 +43,7 @@
</dependencies>
<build>
<sourceDirectory></sourceDirectory>
<!--<sourceDirectory></sourceDirectory>-->
<plugins>
<plugin>
<groupId>org.jetbrains.kotlin</groupId>
......
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