Thomas Girke tgirke
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| ################################################## | |
| ## Create mappability file for reference genome ## | |
| ################################################## | |
| ## Thomas Girke | |
| ## Date: May 16, 2018 | |
| ## PeakSeq docs: | |
| ## https://github.com/gersteinlab/PeakSeq | |
| ## http://gensoft.pasteur.fr/docs/PeakSeq/1.1/PeakSeq.readme | |
| ## Note: mappability step should be skipped in newer version of PeakSeq |
tgirke
/ Jekyll_Doc_Theme.md
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December 8, 2022 19:28
How to set up and maintain Jekyll Documentation Theme
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| x <- 1:12 |
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| ######################################## | |
| ## Import of DrugBank Annotation Data ## | |
| ######################################## | |
| ## Function to import DrugBank XML to data.frame | |
| ## Last step gives error. To debug, the following function may help. | |
| ## Note, this functions needs some major speed improvements. Ideally, | |
| ## it should be replaced with a standard XML import method. | |
| ## (1) Download | |
| ## - download DrugBank XML (https://www.drugbank.ca/releases/latest) | |
| ## - name uncompressed file 'drugbank.xml' |
tgirke
/ Bioconductor_Git_Mirror.md
Last active
April 15, 2020 00:36
How to maintain Bioconductor package on GitHub and keep it in sync with SVN repository on Bioconductor
tgirke
/ qualityTrimming
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May 31, 2016 02:07
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| ##################################### | |
| ## Quality Trimming of FASTQ Reads ## | |
| ##################################### | |
| ## Author: Thomas Girke | |
| ## Last update: May 30, 2016 | |
| ## Usage of below function combined with preprocessReads form systemPipeR: | |
| # qcTrim <- "qualityTrimming(fq, phred_cutoff=20, cutoff_occurrences=1, N_cutoff=1, minreadlength=100)" | |
| # preprocessReads(args=args, Fct=qcTrim, batchsize=100000, overwrite=TRUE, compress=TRUE) | |
| ## Arguments: |
tgirke
/ appendCounter.R
Last active
October 22, 2015 21:35
Append occurrence counter to entries in a character vector
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| ############################ | |
| ## appendCounter Function ## | |
| ############################ | |
| ## Author: Thomas Girke | |
| ## Last update: 04-Oct-15 | |
| ## Function to append occurrence counter to entries in character | |
| ## vector and return the results as named vector where the | |
| ## original data are in the same order in the data slot | |
| ## and the counting result in the name slot. |
tgirke
/ Source_Gist_in_R.R
Last active
August 29, 2015 14:24
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| ############################# | |
| ## Source R code from Gist ## | |
| ############################# | |
| ## Display code snippet as raw by pressing Raw button on top right corner of Gist | |
| ## Save URL in address bar of browser | |
| # library(RCurl) | |
| ## (a) Source specific commit of code | |
| # source(textConnection(getURL("https://gist.githubusercontent.com/tgirke/c26daac0f647f1732a58/raw/521292eca2d4daeab8911df2552f0c55b0e58e6b/Source_Gist_in_R"))) | |
| ## (b) Source latest version of code (delete commit ID in URL after .../raw/...) | |
| # source(textConnection(getURL("https://gist.githubusercontent.com/tgirke/c26daac0f647f1732a58/raw/Source_Gist_in_R"))) |
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| my_frame[!duplicated(my_frame[,2]),] # Removes rows with duplicated values in selected column. | |
| my_frame[my_frame$y2 > my_frame$y3,] # Prints all rows of data frame where values of col1 > col2. Comparison operators are: == (equal), != (not equal), >= (greater than or equal), etc. Logical operators are & (and), | (or) and ! (not). | |
| x <- 0.5:10; x[x<1.0] <- -1/x[x<1.0] # Replaces all values in vector or data frame that are below 1 with their reciprocal value. | |
| x <-data.frame(month=month.abb[1:12], AB=LETTERS[1:2], no1=1:48, no2=1:24); x[x$month == "Apr" & (x$no1 == x$no2 | x$no1 > x$no2),] # Prints all records of frame 'x' that contain 'Apr' AND have equal values in columns 'no1' and 'no2' OR have greater values in column 'no1'. | |
| x[x[,1] %in% c("Jun", "Aug"),] # Retrieves rows with column matches specified in a query vector. | |
| x[c(grep("\\d{2}", as.character(x$no1), perl = TRUE)),] # Possibility to print out all rows of a data frame where a regular expression matches (here all double digit values in col 'no1'). | |
| x[c(g |