BOL: Related items

eFORGE.v1.2

Jit — Fri, 28 Oct 2016 09:06:59 -0500

The eFORGE tool provides a method to view the tissue specific regulatory component of a set of EWAS DMPs. eFORGE analysis takes a set of DMPs, such as those hits above genome-wide significance threshold in an EWAS study, and analyses whether there is enrichment for overlap of putative functional elements compared to matched background DMPs. It assesses enrichment on a per cell type basis, since functional elements are differentially active in different cell types, and hence can expose tissue-specific signals of enrichment for the given test DMP set. This can reveal the sites of action underlying the EWAS signal, and provide confirmation of the validity of the EWAS where a tissue-specific mechanism is known or expected for the phenotype. Conversely unknown tissue involvements can also be revealed.

Address of the bookmark: http://eforge.cs.ucl.ac.uk/eFORGE.v1.2/?documentation

R Graphical Cookbook by Winston Chang

Abhimanyu Singh — Fri, 04 Nov 2016 12:50:30 -0500

R Graphical Cookbook by Winston Chang

A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown in the text of the book, but in most cases the differences will be that these pages contain additional code to lay out multiple plots on a single "page".

The code presented for each figure is self-contained, i.e., all code required to produce the figure is included. This means that there is sometimes considerable overlap of code between several figures In some cases, it may be necessary to install an add-on package from CRAN to get the code to run.

More books at http://www.e-reading.club/bookreader.php/137370/C486x_APPb.pdf

Bookmarks Biostatistics materials and books

Jit — Tue, 08 Nov 2016 07:42:42 -0600

Biostatistics did not spring fully formed from the brow of R. A. Fisher, but evolved over many years. This process is continuing, although it may not be obvious from the outside. It has been ten years since the first edition of this book appeared (and rather longer since it was begun). Over this time, new areas of biostatistics have been developed and emphases and interpretations have changed

Please bookmarks your favourate biostatistics books in commend sectons ...

Address of the bookmark: http://www.cos.ufrj.br/~bioestatistica/livros/Introduction%20to%20Biostatistics.pdf

GoJS

Jit — Tue, 22 Nov 2016 08:25:37 -0600

GoJS is a feature-rich JavaScript library for implementing custom interactive diagrams and complex visualizations across modern web browsers and platforms. GoJS makes constructing JavaScript diagrams of complex nodes, links, and groups easy with customizable templates and layouts.

GoJS offers many advanced features for user interactivity such as drag-and-drop, copy-and-paste, in-place text editing, tooltips, context menus, automatic layouts, templates, data binding and models, transactional state and undo management, palettes, overviews, event handlers, commands, and an extensible tool system for custom operations.

GoJS is pure JavaScript, so users get interactivity without requiring round-trips to servers and without plugins. GoJS normally runs completely in the browser, rendering to an HTML5 Canvas element or SVG without any server-side requirements. GoJS does not depend on any JavaScript libraries or frameworks, so it should work with any HTML or JavaScript framework or with no framework at all.

More at http://gojs.net/latest/index.html

Address of the bookmark: http://gojs.net/latest/index.html

Minia

Jit — Thu, 08 Dec 2016 05:07:00 -0600

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Download

Minia 2.0.7 Linux 64-bits binaries (Source code) (Legacy codebase)

For the impatient

A typical Minia command line looks like:

./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix

Type

./minia

for a quick explanation of the parameters.

For more information, refer to the manual.

KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome size estimation for your dataset.

Address of the bookmark: http://minia.genouest.org/

Velvet tutorial

Poonam Mahapatra — Fri, 09 Dec 2016 04:19:07 -0600

The objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library through the use of Bowtie, the primary parameters of velvet, and the process involved in producing a de novo assembly from Illumina reads.

http://evomics.org/learning/assembly-and-alignment/velvet/

Address of the bookmark: http://evomics.org/learning/assembly-and-alignment/velvet/

E-MEM: Efficient computation of Maximal Exact Matches

Jit — Thu, 15 Dec 2016 09:30:43 -0600

E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes. See the README file for instructions on how to use E-MEM.

E-MEM source code

The source code can be downloaded here.

If you use E-MEM, please cite:

N. Khiste, L. Ilie, E-MEM: Efficient computation of Maximal Exact Matches for very large genomes, Bioinformatics 31(4) (2015) 509 -- 514.

For any questions, please contact Lucian Ilie: ilie@uwo.ca

Address of the bookmark: http://www.csd.uwo.ca/~ilie/E-MEM/

PEAR

Jit — Mon, 19 Dec 2016 09:28:30 -0600

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

Address of the bookmark: http://sco.h-its.org/exelixis/web/software/pear/doc.html

MCscan

Bulbul — Thu, 22 Dec 2016 03:53:58 -0600

MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

More at http://chibba.agtec.uga.edu/duplication/mcscan/

Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

GKNO

Jit — Tue, 17 Jan 2017 03:35:34 -0600

gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

More at http://gkno.me/

Address of the bookmark: http://gkno.me/