The Steep Slope of Bioinformatics!
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The Steep Slope of Bioinformatics!
So much to learn, so little time
Curated by Neelima Sinha
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kWIP: The k-mer Weighted Inner Product, a de novo estimator of genetic similarity

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data - Yu - 2016 - Methods in Ecology and Evolution - Wiley Online Library

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data - Yu - 2016 - Methods in Ecology and Evolution - Wiley Online Library | The Steep Slope of Bioinformatics! | Scoop.it
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UCSF Researchers Discover That Deep Sequencing Is Overkill For Many Applications | RNA-Seq Blog

UCSF Researchers Discover That Deep Sequencing Is Overkill For Many Applications | RNA-Seq Blog | The Steep Slope of Bioinformatics! | Scoop.it
Ability to Extract Patterns From 'Low Resolution' Data Means Deep Sequencing is Overkill for Many Applications, Researchers Say New research by UCSF
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BMC Bioinformatics

BMC Bioinformatics | The Steep Slope of Bioinformatics! | Scoop.it
BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of...
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IRRI - Big data on 3,000 rice genomes available on the AWS Cloud

IRRI - Big data on 3,000 rice genomes available on the AWS Cloud | The Steep Slope of Bioinformatics! | Scoop.it
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Data analysts' dream come true!
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Genomic variation across landscapes: insights and applications - Bragg - 2015 - New Phytologist - Wiley Online Library

Genomic variation across landscapes: insights and applications - Bragg - 2015 - New Phytologist - Wiley Online Library | The Steep Slope of Bioinformatics! | Scoop.it
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SARTools: a DESeq2- and edgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. - PubMed - NCBI

Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. - PubMed - NCBI | The Steep Slope of Bioinformatics! | Scoop.it
Stat Appl Genet Mol Biol. 2010;9:Article39. doi: 10.2202/1544-6115.1585. Epub 2010 Oct 31.
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Draw Venn Diagram

Draw Venn Diagram | The Steep Slope of Bioinformatics! | Scoop.it
Online tool to create custom Venn/Euler diagrams up to 5 sets and intersections for up to 30 sets
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Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Welcome to a Little Book of R for Bioinformatics! — Bioinformatics 0.1 documentation

So useful
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Knowledge units – the atoms of statistical education | Simply Statistics

Knowledge units – the atoms of statistical education | Simply Statistics | The Steep Slope of Bioinformatics! | Scoop.it
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XMRF: an R package to fit Markov Networks to high-throughput genetics data

XMRF: an R package to fit Markov Networks to high-throughput genetics data | The Steep Slope of Bioinformatics! | Scoop.it
Technological advances in medicine have led to a rapid proliferation of high-throughput “omics” data.
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Getting the most out of RNA-seq data with expVIP (Expression Visualization and Integration Platform)

Getting the most out of RNA-seq data with expVIP (Expression Visualization and Integration Platform) | The Steep Slope of Bioinformatics! | Scoop.it
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BMC Bioinformatics

BMC Bioinformatics | The Steep Slope of Bioinformatics! | Scoop.it
BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of...
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Mutual – heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery | RNA-Seq Blog

Mutual – heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery | RNA-Seq Blog | The Steep Slope of Bioinformatics! | Scoop.it
The advance of high-throughput sequencing has made it possible to obtain new transcriptomes and study splicing mechanisms in non-model organisms. In these
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BioTapestry: Version 7.0 Release Notes

BioTapestry: Version 7.0 Release Notes | The Steep Slope of Bioinformatics! | Scoop.it
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For network construction and viewing
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Zbrowse: an interactive GWAS results browser

Zbrowse: an interactive GWAS results browser | The Steep Slope of Bioinformatics! | Scoop.it
The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results.
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Compact graphical representation of phylogenetic data and metadata with GraPhlAn

Compact graphical representation of phylogenetic data and metadata with GraPhlAn | The Steep Slope of Bioinformatics! | Scoop.it
The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata.
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How A Tea Party Turned Into A Scientific Legend

How A Tea Party Turned Into A Scientific Legend | The Steep Slope of Bioinformatics! | Scoop.it
When pouring tea, do you add the tea first or the milk first? If you think it can’t possibly matter, you’re unfortunately wrong — as Dr.
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The Fisher test!
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Learn R for beginners with our PDF

Learn R for beginners with our PDF | The Steep Slope of Bioinformatics! | Scoop.it
It's all here in one place -- our popular "Beginner's guide to using R." You'll learn how to get your data into R, easy ways to do basic data analysis, painless data visualization, syntax quirks you'll want to know and get tons of useful resources.
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