eureka

Collection of useful bits used to elucidate pesky little mysteries

NGS / scRNA-Seq

Getting ZINB-WaVE and Seurat working

• Rmd - https://github.com/c5creative/eureka/blob/master/zinbwave-seurat.rmd
• KnitR - http://htmlpreview.github.io/?https://github.com/c5creative/eureka/blob/master/zinbwave-seurat.html

NGS / RNA-Seq

Mapped reads disappear when counting reads (HT-Seq, FeatureCouts)

• https://www.biostars.org/p/117363/
• https://www.biostars.org/p/110352/

Batch effects in RNA-Seq

In DESeq2

From Michael Love (DESeq2) - https://support.bioconductor.org/p/76099/

Batch effects are gene-specific, and DESeq2 fits gene-specific coefficients for the batch term. If you want to get an idea how much batch variability contributes to a PCA plot, I've recommended the following approach on the support site before: variance stabilize the counts, apply limma's removeBatchEffect to assay(vsd), then use plotPCA to plot the residuals.

# Make some simulated data with a batch effect:
dds <- makeExampleDESeqDataSet(betaSD=1,interceptMean=10)
dds$batch <- factor(rep(c("A","B"),each=6))

# VST, remove batch effect, then plotPCA:

vsd <- vst(dds)
plotPCA(vsd, "batch")
assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$batch)
plotPCA(vsd, "batch")

DASC

DASC is an R package used for identifying batches and classifying samples into different batches in a high dimensional gene expression dataset. The batch information can be further used as a covariate in conjunction with other variables of interest among standard bioinformatics analysis like differential expression analysis. https://github.com/zhanglabNKU/DASC

R

Rtools 3.5 is incompatible with R 3.5 in Windows

Fix posted at https://community.rstudio.com/t/error-dependency-transformr-is-not-available-for-package-gganimate/11134/3

# Set path of Rtools
Sys.setenv(PATH = paste(Sys.getenv("PATH"), "*InstallDirectory*/Rtools/bin/",
                       "*InstallDirectory*/Rtools/mingw_64/bin", sep = ";")) #for 64 bit version
Sys.setenv(BINPREF = "*InstallDirectory*/Rtools/mingw_64/bin")
library(devtools)

#Manually "force" version to be accepted 
assignInNamespace("version_info", c(devtools:::version_info, list("3.5" = list(version_min = "3.3.0", version_max = "99.99.99", path = "bin"))), "devtools")
find_rtools() # is TRUE now

# Now you can install transformr then gganimate
devtools::install_github("thomasp85/transformr")
devtools::install_github("dgrtwo/gganimate")

Random links

• https://hbctraining.github.io/DGE_workshop/lessons/05_DGE_DESeq2_analysis2.html
• https://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data/
• https://drsimonj.svbtle.com/visualising-residuals
• VMware/Ubuntu18.10 full screen issue fix -- vmware/open-vm-tools#303
• Ubuntu 18.* - https://askubuntu.com/questions/967842/how-to-remove-phone-style-gnome-swipe-to-unlock remove annoying screen 'lock/swipe'

Windows

Add a new filetype to the right-click context menu

1. Open registry editor
2. go to HKEY_CLASSES_ROOT, look for filetype to add to menu
3. Right click on it, create new KEY, name it ShellNew
4. Right click new key, select New | String Value, assign it a value of NullFile, then right click it and assign the data to 1