BOL: Related items

OpenCPU

Rahul Nayak — Sun, 05 Jul 2015 18:34:46 -0500

OpenCPU is a system for embedded scientific computing and reproducible research. The OpenCPU server provides a reliable and interoperable HTTP API for data analysis based on R.

The OpenCPU JavaScript client library provides the most seamless integration of R and JavaScript available today.

OpenCPU uses standard R packaging to develop, ship and deploy web applications. Several open source example apps are available from Github.

Installing your own OpenCPU server is super easy and only takes a few minutes.

More at https://www.opencpu.org/

BioToolbox

Jit — Fri, 19 Feb 2016 09:14:44 -0600

This is a collection of libraries and high-quality end-user scripts for bioinformatic analysis, including working with gene annotation, collecting data scores from a variety of modern file formats, and conversion between file formats. The Bio::ToolBox libraries provide a unified, abstracted interface to multiple common gene annotation formats and the collection of data from multiple data files. They rely on BioPerl SeqFeature libraries and related adaptors to access binary file formats including Bam, BigWig, BigBed, and USeq. The Bio::ToolBox package includes scripts for setting up databases of annotation, collecting annotated features, collecting genomic data relative to features, manipulating and analyzing data, and data format conversion.

More at http://cpansearch.perl.org/src/TJPARNELL/

Address of the bookmark: http://cpansearch.perl.org/src/TJPARNELL/

GATB : Genome Analysis Toolbox with de-Bruijn graph

Jit — Thu, 28 Apr 2016 11:16:51 -0500

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

Samtools Primer !!

Jit — Thu, 23 Jun 2016 07:18:17 -0500

SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.

keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introduction
Revisions

    1.0: May 30, 2013: First public release on biobits.org.
    1.1: July 24, 2013: Updated with Disqus Comments / Feedback section.
    1.2: December 19, 2014: Multiple updates, including:
        Updated to use samtools 1.1 and bcftools 1.2.
        Updated usage for bcftools.

About

SAMtools is a popular open-source tool used in next-generation sequence analysis. This primer provides an introduction to SAMtools, and is geared towards those new to next-generation sequence analysis. The primer is also designed to be self-contained and hands-on, meaning that you only need to install SAMtools, and no other tools, and sample data sets are provided. Terms in bold are also explained in the glossary at the end of the document.

Address of the bookmark: http://biobits.org/samtools_primer.html

Fools guide

Poonam Mahapatra — Sun, 02 Apr 2017 14:31:18 -0500

This website and accompaning documents are intended as a tool to help researchers dealing with non-model organisms acquire and process transcriptomic high-throughput sequencing data without having to learn extensive bioinformatics skills. It covers all steps from tissue collection, sample preparation and computer setup, through addressing biological questions with gene expression and SNP data.

http://sfg.stanford.edu/denovo.html

http://sfg.stanford.edu/sequencing.html

http://sfg.stanford.edu/BLAST.html

http://sfg.stanford.edu/denovo.html

Address of the bookmark: http://sfg.stanford.edu/guide.html

SciLifeLab tutorial for bioinformatics analysis !

Jit — Tue, 17 Apr 2018 04:33:00 -0500

SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.

Courses

Old courses (2012-2014)

A simple tutorial for a complex ComplexHeatmap

Neel — Fri, 02 Apr 2021 06:18:32 -0500

ComplexHeatmap (Gu, Eils, and Schlesner (2016)) is an R Programming Language (R Core Team (2020)) package that is currently listed in the Bioconductor package repository.

install and load required packages

  require(RColorBrewer)
  require(ComplexHeatmap)
  require(circlize)
  require(digest)
  require(cluster)

If all load successfully, proceed to Part 3. Otherwise, go through the following code chunks in order to ensure that each package is installed and loaded properly.

BiocManager (Morgan (2019))

Address of the bookmark: https://github.com/kevinblighe/E-MTAB-6141

Biological file format tutorial

Jit — Sun, 17 Dec 2017 18:13:03 -0600

This section explains some of the commonly used file formats in bioinformatics. The information provided here is basic and designed to help users to distinguish the difference between different formats. Please refer user manual or other information resources on web for more details.

Address of the bookmark: https://bioinformatics.uconn.edu/resources-and-events/tutorials/file-formats-tutorial/

Machine learning training and courses in bioinformatics !

Rahul Nayak — Tue, 31 Dec 2019 19:33:07 -0600

Machine learning techniques have been successful in analyzing biological data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. In this class, we will learn basics about probabilistic models and machine learning techniques. We will focus on probabilistic models (Markov models, Hidden Markov models, and Bayesian networks) for biological sequence analysis and systems biology. Other machine learning techniques, such as Naive bayes, neural networks and SVMs will only be covered briefly.

More at http://homes.sice.indiana.edu/yye/lab/teaching/spring2017-I529/

Pangolin tutorial !

Abhi — Fri, 10 Dec 2021 05:58:59 -0600

This is a tutorial for using the Pangolin Web Application. For information on using the command line tool, please visit the command line tool usage page.

https://cov-lineages.org/resources/pangolin/tutorial.html

Address of the bookmark: https://cov-lineages.org/resources/pangolin/tutorial.html

BOL: Related items

OpenCPU

BioToolbox

GATB : Genome Analysis Toolbox with de-Bruijn graph

Samtools Primer !!

Fools guide

SciLifeLab tutorial for bioinformatics analysis !

Courses

Metagenomics Workshop

Introduction to Bioinformatics Using NGS Data

Introduction to Genome Annotation

De Novo Genome Assembly

RNA-seq course

R Programming Foundations for Life Scientists

Single cell RNA sequencing analysis

A simple tutorial for a complex ComplexHeatmap

Biological file format tutorial

Machine learning training and courses in bioinformatics !

Pangolin tutorial !