BOL: Related items

RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)

Surabhi Chaudhary — Fri, 28 Feb 2020 23:27:37 -0600

RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows.

Single-SNP GWAS with RGWAS.normal function
SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests multiple SNPs at the same time)
Check epistatic (SNP-set x SNP-set interaction) effects with RGWAS.epistasis (very slow and less reliable)

https://github.com/KosukeHamazaki/RAINBOWR

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007663

https://cran.r-project.org/web/packages/RAINBOWR/index.html

Address of the bookmark: https://github.com/KosukeHamazaki/RAINBOWR

Platypus – R package for object detection and image segmentation.

BioStar — Mon, 09 Nov 2020 02:56:25 -0600

platypus is an R package for object detection and semantic segmentation. Currently using

platypus you can perform:

multi-class semantic segmentation using U-Net architecture
multi-class object detection using YOLOv3 architecture

You can install the latest version of platypus with remotes package:

remotes::install_github("maju116/platypus")

Note that in order to install platypus you need to install keras and tensorflow packages and Tensorflow version >= 2.0.0 ( Tensorflow 1.x will not be supported!)

Address of the bookmark: https://github.com/maju116/platypus

R Shiny in Life Sciences – Top 7 Dashboard Examples

Neel — Fri, 01 Apr 2022 19:05:03 -0500

R Shiny is one of the easiest ways for developers to make production-ready dashboards when speed and functionality are crucial. Shiny is approachable with a lot of documentation available, and because of this, a lot of developers/researchers with non-coding backgrounds are able to produce some impressive results. The whole ecosystem is easy to get your head around and pretty much limitless with regard to what you can do.

Address of the bookmark: https://www.r-bloggers.com/2022/03/r-shiny-in-life-sciences-top-7-dashboard-examples/

SVbyEye: R Package to visualize alignments between two or multiple DNA sequences

LEGE — Tue, 17 Sep 2024 02:34:57 -0500

R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex SVs in the context of sequence homology helping resolve the mechanisms underlying their formation. Availability and implementation SVbyEye is available at https://github.com/daewoooo/SVbyEye.

Author: David Porubsky

Address of the bookmark: https://github.com/daewoooo/SVbyEye

Added video feature in BOL

Jitendra Narayan — Tue, 13 Aug 2013 17:42:16 -0500

Just in: Added video features in BOL, now you can watch and share your favourite bioinformatics video tutorials.

Share your favourite video tutorial or lectures on BOL at http://bioinformaticsonline.com/videolist/all . You can also add video in you groups.

Note: Other than bioinformatics video material/tutorial will be deleted without any prior warning.

Perl and BioPerl Tutorials

Jitendra Narayan — Wed, 28 Aug 2013 05:51:38 -0500

This bookmark is created to store the useful Perl and BioPerl tutorial links at one place. Feel free to share and add more useful tutorial links here ....

Address of the bookmark: http://cbb.sjtu.edu.cn/course/database/beginning.pdf

Bioinformatics algorithms tutorials

John Parker — Tue, 24 Jun 2014 00:10:45 -0500

Useful bioinformatics tutorial, such as

De Bruijn Graphs for NGS Assembly
Algorithms for PacBio Reads
Software and Hardware Concepts for Bioinformatics
Finding us in Homolog.us (Search Algorithms)
NGS Genome and RNAseq Assembly - a Hands on Primer
Introduction to PERL, Python, R and C/C++ for Bioinformatics

Address of the bookmark: http://www.homolog.us/Tutorials/

Microscope

Jitendra Narayan — Fri, 04 Mar 2016 05:26:31 -0600

Microscope Platform user documentation.

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html

Understanding Fastqc Output

Jit — Fri, 15 Apr 2016 05:47:40 -0500

Understanding Following table and graphs

Duplication level
kmer profile
per base GC content
per base N content
per base quality
per base sequence content
per sequence GC content
per sequence quality
sequence length distribution

More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

Linux command line exercises for NGS data processing

Jit — Wed, 22 Jun 2016 07:59:39 -0500

The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing inside:

[uzi@quince-srv2 ~/]$ cp -r /home/opt/MScBioinformatics/linuxTutorial .
[uzi@quince-srv2 ~/]$ cd linuxTutorial
[uzi@quince-srv2 ~/linuxTutorial]$

I have deliberately chosen Awk in the exercises as it is a language in itself and is used more often to manipulate NGS data as compared to the other command line tools such as grep, sed, perl etc. Furthermore, having a command on awk will make it easier to understand advanced tutorials such as Illumina Amplicons Processing Workflow.

In Linux, we use a shell that is a program that takes your commands from the keyboard and gives them to the operating system. Most Linux systems utilize Bourne Again SHell (bash), but there are several additional shell programs on a typical Linux system such as ksh, tcsh, and zsh. To see which shell you are using, type

[uzi@quince-srv2 ~/linuxTutorial]$ echo $SHELL

/bin/bash

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html