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Rescooped by Mel Melendrez-Vallard from Bioinformatics Training
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abSYNTH Bioinformatics Tools

abSYNTH Bioinformatics Tools | Bioinformatics Software: Sequence Analysis | Scoop.it

Via Costas Bouyioukos, Pedro Fernandes
Mel Melendrez-Vallard's insight:

well that's neat.

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Costas Bouyioukos's curator insight, March 26, 4:31 AM

Our tutorial on tools for the systematic analysis of periodicities on genomic sequences run (almost) smoothly yesterday at the 2014 aSSB Evry Thematic School.

 

Find the tools of MEGA team on iSSB webtools server https://absynth.issb.genopole.fr/Bioinformatics/

under the systems biology section.
(registration, simple and free, is required)

Bioinformatics Software: Sequence Analysis
Research and postings on the latest in bioinformatic analysis software that's out there/published and open source. Let's not re-invent the wheel. Disclaimer: I do not promote one software over the next, you'll have to evaluate software on your own.
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Bioinformatics tools extracted from a typical mammalian genome project | The OpenHelix Blog

Bioinformatics tools extracted from a typical mammalian genome project | The OpenHelix Blog | Bioinformatics Software: Sequence Analysis | Scoop.it
In this extended blog post, I describe my efforts to extract the information about bioinformatics-related items from a recent genome sequencing paper, and the
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MeDIP-seq data analysis – diffReps

MeDIP-seq data analysis – diffReps | Bioinformatics Software: Sequence Analysis | Scoop.it
MeDIP-seq (and this should be the same for methylCap-seq/MBD-seq which I’m told is better) is advertised as reasonable cost-effective method to find differentially methylated regions (DMRs).
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EPGA: de novo assembly using the distributions of reads and insert size

RT @SAGRudd: EPGA: de novo assembly using the distributions of reads and insert size http://t.co/OgsLvz71St
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The Genome Factory: Minimum standards for bioinformatics command line tools

Minimum standards for bioinformatics command line tools
by @torstenseemann
via @kbradnam and @RoyChaudhuri
http://t.co/0ftRZHMIb4
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The HIV Mutation Browser: A Resource for Human ...

PLOS Computational Biology is an open-access
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Hierarchical Clustering with R (feat. D3.js and Shiny)

Hierarchical Clustering with R (feat. D3.js and Shiny) | Bioinformatics Software: Sequence Analysis | Scoop.it
(This article was first published on joy of data » R, and kindly contributed to R-bloggers)
Agglomerative hierarchical clustering is a simple, intuitive and well-understood method for clustering data points.
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User friendly RNA-seq differential expression analysis with Degust

User friendly RNA-seq differential expression analysis with Degust | Bioinformatics Software: Sequence Analysis | Scoop.it
There is a need to make bioinformatics tools more user friendly and accessible to a wider audience.
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Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference

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AKE - the Accelerated k -mer Exploration web-tool for rapid taxonomic classification and visualization

Background:
With the advent of low cost, fast sequencing technologies metagenomic analyses are made possible.
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MPAgenomics: an R package for multi-patient analysis of genomic markers

Background:
Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures.
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Webinar - A Submitter's Guide to GenBank: Using BankIt for Small-Scale Nucleotide Sequence Submissions

On December 17th 1:00 PM - 2:00 PM EST, The National Center for Biotechnology Information (NCBI) will present a webinar entitled "A Submitter's Guide to GenBank: Using BankIt for Small-Scale Nucleo...
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ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing

ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing http://t.co/YJGxdlDR3P
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MPAgenomics: an R package for multi-patient analysis of genomic markers

Background:
Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures.
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CompPhy: a web-based collaborative platform for comparing phylogenies

Background:
Collaborative tools are of great help in conducting projects involving distant workers.
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ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation

by Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P.
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A metagenomic pipeline integrating predictive profiling methods and complex networks for the analysis of NGS microbiome data

A metagenomic pipeline integrating predictive profiling methods and complex networks for the analysis of NGS microbiome data
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New Package: partools

(This article was first published on Mad (Data) Scientist, and kindly contributed to R-bloggers)
I mentioned last week that I would be putting together a package, based in part on my posts on Snowdoop.
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Rescooped by Mel Melendrez-Vallard from Virology and Bioinformatics from Virology.ca
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ECOD: An Evolutionary Classification of Protein Domains

PLOS Computational Biology is an open-access

Via Chris Upton + helpers
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Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools

Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools | Bioinformatics Software: Sequence Analysis | Scoop.it
Incremental joint variant calling
Variant calling in large populations is challenging due to the difficulty in providing a consistent set of calls at all possible variable positions.
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F1000Research Article: Rampant software errors undermine scientific results.

Read the latest article version by David A. W. Soergel, at F1000Research.
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Masking as an effective quality control method for next-generation sequencing data analysis

Background:
Next generation sequencing produces base calls with low quality scores that can affect the accuracy of identifying simple nucleotide variation calls, including single nucleotide polymorphisms and small insertions and deletions.
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Background:
With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important.
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solGS: a web-based tool for genomic selection

Background:
Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods.
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NCBIminer: Sequences harvest from Genbank

NCBIminer is freely available, cross-platform and user-friendly software for mining nucleotide sequence data from GenBank.
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A CRISPR blog / bibliography: COSMID, a tool to find #CRISPR off-targets including indels (usually not found w/other tools).

COSMID, a tool to find #CRISPR off-targets including indels (usually not found w/other tools).: From Georgia T... http://t.co/j8Bj0zjyRb
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