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License: GNU General Public License v3.0
An R meta-package for the analysis of Next Generation Sequencing data
License: GNU General Public License v3.0
Better visualisation of groups in the dendrogram.
library(scater)
rownames(sce) <- uniquifyFeatureNames(rowData(sce)$ENSEMBL, rowData(sce)$SYMBOL)
When parallelisation is possbile, "Tools/sambamba" has better performance.
QL as the default.
For the up- and downregulated genes separately, run a Fisher's exact
test to see if the regulated genes overlap with the high/low GC, short
long genes. i.e.
gcTypes = data.frame("GC < 0.4"=as.numeric(rowData(rawData)$gc) < 0.4,
"GC > 0.6"=as.numeric(rowData(rawData)$gc) > 0.6,
check.names=FALSE)
widthTypes = data.frame("width <
800nt"=as.numeric(rowData(rawData)$width) < 800,
"width >
2000nt"=as.numeric(rowData(rawData)$width) > 2000,
check.names=FALSE)
That should be part of the report. If there is a significant overlap.
The result is suspicious and potentially an artefact.
Hi,
What is the best way to build vignette for ezRun.
emapplot
from clusterProfiler is problematic.
Disable it for now.
It uses ggplot style igraph (ggraph) to plot the network. Need more time to debug
Example:
https://fgcz-sushi.uzh.ch/projects/p2729/DESeq2_26428_7--over--5_2018-05-06--12-42-45/scripts
RNABamStats
Match Count Percentage table.
Example:
https://fgcz-gstore.uzh.ch/projects/p2578/RNABamStats_22125_2017-11-06--13-42-26/RNA_BAM_Statistics/00index.html
When the "Read Count" column is absent from the dataset definition, the app stops with
Error in `$<-.data.frame`(`*tmp*`, removed, value = integer(0))
I suspect this is due too this part of the app:
Lines 88 to 100 in 6992d62
(More specifically line 93)
I haven't tried, but putting it under the line 88 conditional could probably solve the issue; alternatively, making Read Count
a necessary column (e.g. in the sushi app) obviously does solve the problem.
clean if not needed.
During installation,
Note: possible error in 'DADA2CreateSeqTab(sampleName, ': unused arguments (maxLen, minLen, isPaired)
Why there are warnings from RnaBamStats app? possibly from getRangesCoverage.
The results looks fine.
40: In setUnlistDataNames(x@unlistData, x@partitioning, use.names, ... :
failed to set names on the unlisted CompressedRleList object
Add fisher.test in samples merging report
Do Per-sample 2-pass mapping for now.
Multi-sample 2-pass mapping is not feasible with current sushi star mapping setup.
BP-d3--over--BL-enrichBoth.txt
Better colourscale
The order of groups might be simply controlled by order(param$grouping)
. It should be always in the order of param$sampleGroup
first, then param$refGroup
.
Description of figures and files.
MergeBamAlignment keeps the full sequence from uBam and adjusted the CIGAR.
The CIGAR is wrong when aligned to negative strand and shows mismatches in browser.
Possibility of adding crosstalk functionality
https://rstudio.github.io/crosstalk/
Add gene name to this file.
Remove
Differential expression test: | QL |
---|
Also use GO ID
Current fastICA implementation takes too much memory for large amount of cells.
determine based on gene's chr.
Need a faster implementation.
Example:
setwd("/scratch/gtan/debug/p2710-CountQC")
library(ezRun)
param = list()
param[['cores']] = '1'
param[['ram']] = '2'
param[['scratch']] = '10'
param[['node']] = ''
param[['process_mode']] = 'DATASET'
param[['name']] = 'Count_QC'
param[['refBuild']] = 'p2710_Perma/FGCZ/Metabat_20180427/Annotation/Release_2018_04_30'
param[['refFeatureFile']] = 'genes.gtf'
param[['featureLevel']] = 'gene'
param[['normMethod']] = 'logMean'
param[['runGO']] = 'true'
param[['backgroundExpression']] = '10'
param[['transcriptTypes']] = ''
param[['specialOptions']] = ''
param[['expressionName']] = ''
param[['mail']] = '[email protected]'
param[['dataRoot']] = '/srv/gstore/projects'
param[['resultDir']] = 'p2710/CountQC_26335_2018-05-05--15-31-20'
output = list()
output[['Name']] = 'Count_QC'
output[['Species']] = 'NA'
output[['refBuild']] = 'p2710_Perma/FGCZ/Metabat_20180427/Annotation/Release_2018_04_30'
output[['Static Report [Link]']] = 'p2710/CountQC_26335_2018-05-05--15-31-20/Count_QC/00index.html'
output[['Live Report [Link]']] = 'http://fgcz-shiny.uzh.ch/fgcz_exploreCountQC_app/?data=p2710/CountQC_26335_2018-05-05--15-31-20/Count_QC/counts-qjliarzqgzfz-EzResult.RData'
output[['Report [File]']] = 'p2710/CountQC_26335_2018-05-05--15-31-20/Count_QC'
input = '/srv/gstore/projects/p2710/CountQC_26335_2018-05-05--15-31-20/input_dataset.tsv'
EzAppCountQC$new()$run(input=input, output=output, param=param)
Use scater implementation
For faster TSNE plot
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