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Bioinformatics Miscellaneous

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Installing R packages. Part of the reason R has become so popular is the vast array of packages available at the cran and bioconductor repositories.

Installing R packages

In the last few years, the number of packages has grown exponentially! This is a short post giving steps on how to actually install R packages. Let’s suppose you want to install the ggplot2 package. Well nothing could be easier. We just fire up an R shell and type: > install.packages("ggplot2") In theory the package should just install, however: if you are using Linux and don’t have root access, this command won’t will be asked to select your local mirror, i.e. which server should you use to download the package. Biometric Research Branch home page. Htseq Count. 3.1 years ago by United States Hello Everyone I am working on RNA seq data.

Htseq Count

Visualizing Chip-Seq And Bis-Seq (Dna Methylation) Data. A tour through HTSeq — HTSeq 0.6.1p2 documentation. In the analysis of high-throughput sequencing data, it is often necessary to write custom scripts to form the “glue” between tools or to perform specific analysis tasks.

A tour through HTSeq — HTSeq 0.6.1p2 documentation

HTSeq is a Python package to facilitate this. This tour demonstrates the functionality of HTSeq by performing a number of common analysis tasks: Getting statistical summaries about the base-call quality scores to study the data quality.Calculating a coverage vector and exporting it for visualization in a genome browser.Reading in annotation data from a GFF file.Assigning aligned reads from an RNA-Seq experiments to exons and genes. Untitled. Completion of genome duplication is challenged by structural and topological barriers that impede progression of replication forks.


Although this can seriously undermine genome integrity, the fate of DNA with unresolved replication intermediates is not known. Here, we show that mild replication stress increases the frequency of chromosomal lesions that are transmitted to daughter cells. Throughout G1, these lesions are sequestered in nuclear compartments marked by p53-binding protein 1 (53BP1) and other chromatin-associated genome caretakers. We show that the number of such 53BP1 nuclear bodies increases after genetic ablation of BLM, a DNA helicase associated with dissolution of entangled DNA. [ensembl-dev] rRNA genes. Rrna Removal In Rna-Seq Data. 19 months ago by.

Rrna Removal In Rna-Seq Data

Housekeeping Genes. List of housekeeping human genes derived from the article "Human Housekeeping genes are compact," published in Trends in Genetics 19, 362-365 (2003).

Housekeeping Genes

Each gene name/description is followed by its geometric average expression level according to the data published by Su et al. GENCODE - Gencode gene/transcript biotypes description. Please also compare to the VEGA descriptions Further details about the annotation of non-coding RNAs are listed on this Ensembl page Gencode GTF format description.

GENCODE - Gencode gene/transcript biotypes description

QuickNGS - All-in-one data processing for Next-Generation Sequencing. This article was previously published under Q214204 You can use the special characters listed in the "More Information" section of this article with the Find and Replace commands on the Edit menu.

R Function of the Day. CellNet: CellNet. BiocViews. RNA-Seq, generate batch-free count matrix. R: Remove Batch Effect. Description Remove batch effects from expression data.

R: Remove Batch Effect

Usage removeBatchEffect(x, batch=NULL, batch2=NULL, covariates=NULL, design=matrix(1,ncol(x),1), ...) Arguments Details This function is useful for removing batch effects, associated with hybridization time or other technical variables, prior to clustering or unsupervised analysis such as PCA, MDS or heatmaps. The design matrix is used to describe comparisons between the samples, for example treatment effects, which should not be removed.

The function (in effect) fits a linear model to the data, including both batches and regular treatments, then removes the component due to the batch effects. The data object x can be of any class for which lmFit works. Value A numeric matrix of log-expression values with batch and covariate effects removed. Merge - Merging more than 2 dataframes in R by rownames. Getting Genetics Done: Merging data from different files using R. A reader asked yesterday how you would merge data from two different files.

Getting Genetics Done: Merging data from different files using R

For example, let's say you have a ped file with genotypes for individuals, and another file that had some other data for some of the individuals in the pedfile, like clinical or environmental covariates. How would you go about automatically putting the clinical data from file 2 into the appropriate rows in file 1? Without using a database, the easiest way is probably using the "merge" function in R that will do the trick with a one-line command. Here's a short tutorial to get you started. First, start up R on the cheeses simply by typing in the uppercase letter R and hit enter. Read.table("

R gsub Function Examples. R gsub Function gsub() function replaces all matches of a string, if the parameter is a string vector, returns a string vector of the same length and with the same attributes (after possible coercion to character). Elements of string vectors which are not substituted will be returned unchanged (including any declared encoding). gsub(pattern, replacement, x, = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE) • pattern: string to be matched • replacement: string for replacement • x: string or string vector • if TRUE, ignore case... RNA-Seq Alignment and Visualization. Normalization of RNAseq Data. Convert CSV file to FASTA. R - How can I view the source code for a function? [ensembl-dev] biomart down? Thomas Maurel maurel at Sat Feb 15 21:01:38 GMT 2014 Dear Paul, The BiomaRt package from Bioconductor is pointing to by default (which seems to be down at the moment), could you please report this issue to the user list (biomart-users at as we don't look after the website.

Ensembl id conversion. WEHI Bioinformatics - A RNA-seq Case Study. A Bioconductor RNA-seq pipeline Here we illustrate how to use two Bioconductor packages - Rsubread and limma - to perform a complete RNA-seq analysis, including Subread read mapping, featureCounts read summarization, voom normalization and limma differential expresssion analysis. Case study Data and software. The RNA-seq data used in this case study include four libraries: A_1, A_2, B_1 and B_2. A_1 and A_2 are both Universal Human Reference RNA (UHRR) samples but they underwent separate sample preparation. After downloading the data package, uncompress it (do not uncompress the .gz files included in the data package) and save it to your current working directory. If the required Bioconductor libraries were not installed in your R, you can issue the following commands under your R prompt to install them: Data processing and analysis of genetic variation using next-gen sequencing (2012)

Homer Software and Data Download. Where *.bt2 files that were created using the bowtie2-build command in step 1, or from a downloaded index. If the *.bt2 files are stored int the "/path-to-bowtie2-program/indexes/" directory, you only need to specify the name of the index. If the index files are located elsewhere, you can specify the full path names of the index files (in the examples above this would be "-x /programs/indexes/hg19"). In the example above, we use 8 processors/threads. The bowtie2 program is very parallel in nature, with near linear speed up with additional processors. The default output is a SAM file. The Simple Fool's Guide - Quality Control. Untitled. Unix & Perl Primer for Biologists. We have written a basic introductory course for biologists to learn the essential aspects of the Perl programming language.

This started as a course for grad students at UC Davis, and we then ran it as a one week intensive course for anyone on campus who was interested (sponsored by the UC Davis Genome Center). The feedback from these courses was very positive and so we have decided that we should make it available to anyone who is interested. The course is very much aimed at people with no prior experience in either programming or Unix. It is increasingly common that biologists have to deal with vast amounts of in silico data as part of their research, often in the form of many large text files that are the output from research equipment or computer programs.

If you complete this course you will hopefully learn enough to be able to write programs to interrogate, refine, and process such data.