tgirke / SDFstreamer.R

Created September 15, 2012 19:36

ChemmineR To-Dos

	#####################################################
	## (A) Add fingerprint folding argument to desc2fp ##
	##########################################
	## Intersect and Venn Diagram Functions ##
	##########################################
	## Author: Thomas Girke
	## Last update: March 24, 2012
	## Utilities:
	## (1) Venn Intersects
	## Computation of Venn intersects among 2-20 or more sample sets using the typical

tgirke / gist:4101283

Created November 17, 2012 23:16

test

	#####################################################
	## (A) Add fingerprint folding argument to desc2fp ##
	##########################################
	## Intersect and Venn Diagram Functions ##
	##########################################
	## Author: Thomas Girke
	## Last update: March 24, 2012
	## Utilities:
	## (1) Venn Intersects
	## Computation of Venn intersects among 2-20 or more sample sets using the typical

tgirke / test.R

Created November 18, 2012 00:31

test

	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

tgirke / Source_Gist_in_R.R

Last active August 29, 2015 14:24

	#############################
	## 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")))

tgirke / appendCounter.R

Last active October 22, 2015 21:35

Append occurrence counter to entries in a character vector

	############################
	## 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 / gist-markdown-template.md

Last active April 4, 2023 00:51

Gist Markdown Template

Project Name

TODO: Write a project description

Installation

TODO: Describe the installation process

Usage

tgirke / qualityTrimming

Last active May 31, 2016 02:07

	#####################################
	## 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 / 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

Maintain Bioconductor Package on GitHub

Table of Content

Overview
Script to create/update Bioc branches
Create GitHub repository of your package
Commit changes to GitHub and Bioc SVN
Update repository after a new Bioconductor release

tgirke / DrugBank2SQLite.R

Last active July 28, 2023 06:17

Import DrugBank to SQLite

	########################################
	## 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 / test.R

Created October 25, 2016 20:54

delete

x <- 1:12

Thomas Girke tgirke

Project Name

Installation

Usage

Maintain Bioconductor Package on GitHub

Table of Content