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mblondel/statistical_tests.py

t-test and wilcoxon-test examples in Python - Gist is a simple way to share snippets of text and code with others.

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Let's say your data has been treated with python and you want to do some statistical tests, but you don't want to add R language ?  Well, get started to statistical tests with numpy !!

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csvsimple

csvsimple | Bioinformatics tools | Scoop.it
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So, you want to write your PhD thesis in LaTeX but you have tons of tables ? I know how making tables in LaTeX is such a pain in the ... Here's one guys example using #csvsimple to ease your pain and help you make beautiful documents !

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The Secret of Self-Regulated Learning

The Secret of Self-Regulated Learning | Bioinformatics tools | Scoop.it
Self-regulated learning is like your own little secret. It stirs from within you, and is the voice in your head that asks you questions about your learning.

More formally, self-regulated learning is the conscious planning, monitoring, evaluation, and ultimately control of one’s learning in order to maximize it. It’s an ordered process that experts and seasoned learners like us practice automatically. It means being mindful, intentional, reflective, introspective, self-aware, self-controlled, and self-disciplined about learning, and it leads to becoming self-directed.
rougeforfire's insight:

Most of you learned bioinformatics on your own, and we expect biologists to keep learning by themselves.. So what is it missing ? There are tons of tutorials, and some have good will.. so.. what about a more specialised pedagogic approach ?

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A brief introduction to "apply" in R

A brief introduction to "apply" in R | Bioinformatics tools | Scoop.it
At any R Q&A site, you'll frequently see an exchange like this one: Q: How can I use a loop to [...insert task here...] ? A: Don't. Use one of the apply functions. So, what are these wondrous a...
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Making loops in R is not optimal, you sould xapply it. I still don't get it, if we can do the same much easier on Python.. but still... Give it a shot if you'd like, the author of this blog is pretty good explaining.

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A Statistical Analysis of the Work of Bob Ross

A Statistical Analysis of the Work of Bob Ross | Bioinformatics tools | Scoop.it
Bob Ross was a consummate teacher. He guided fans along as he painted "happy trees," "almighty mountains" and "fluffy clouds" over the course of his 11-year television career on his PBS show, “The ...
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Learning happy statistics with Bob Ross

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Introduction à la ligne de commande | bioinfo-fr.net

Introduction à la ligne de commande | bioinfo-fr.net | Bioinformatics tools | Scoop.it
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Vos premiers pas dans une console ? Mieux vaut les faire bien accompagnés par l'équipe de bioinfo-fr !

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Rescooped by rougeforfire from Bioinformatics Software: Sequence Analysis
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Learn Basic Linux Commands with This Downloadable Cheat Sheet

Learn Basic Linux Commands with This Downloadable Cheat Sheet | Bioinformatics tools | Scoop.it
Master the command line and you'll be able to perform powerful tasks with just a few keystrokes. This cheat sheet will help you remember helpful Linux commands, whether you're new to Linux or could just use a refresher.

Via Mel Melendrez-Vallard
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Impress biologists, even faster !

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It is time for RData files to become the standard for Data Transfer

It is time for RData files to become the standard for Data Transfer | Bioinformatics tools | Scoop.it
It is time Rdata files become the primary means of disseminating publicly available data online.1. R is the most efficient Statistical software at compressing d

Via Niklaus Grunwald
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Your csv is too big to sennd/keep/submit ? Give a shot to Rdata type !!

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20 Handy Mavericks Tips & Tricks You Probably Don’t Know

20 Handy Mavericks Tips & Tricks You Probably Don’t Know | Bioinformatics tools | Scoop.it
Many would have upgraded to Mavericks by now as it was made available as a free upgrade to all Mac users. While the upgrades from Mountain Lion weren’t as groundbreaking (or as polarizing) as Apple’s iOS 6 upgrade to iOS 7, Mavericks does have many cool new features. After playing ... Continue reading »
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Tired of notifications ?  Do you feel your mac is less reactive  after Maveriks upgrade ? Check out why, and fix it if you need to. Feel fine with your working tool to make a good job !

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Compress PDF – Reduce your PDF Online for Free

Compress PDF – Reduce your PDF Online for Free | Bioinformatics tools | Scoop.it
No file size limits, no ad watermarks - just a free, beautiful and simple online pdf compressor to reduce the size of your PDFs and maintain good quality.
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So you finished your amazing report but it is way too big to mail it.. First of all you should have used LaTeX. If you didn't, take a look to this free online service. You can create your pdf, merge, modify and of course make it lighter.

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Non-uniform coverage of transcripts in RNA-Seq experiments

Non-uniform coverage of transcripts in RNA-Seq experiments | Bioinformatics tools | Scoop.it
Hui Jiang and Julia Salzman have posted a new paper on the arXiv proposing a novel approach to correcting for non-uniform coverage of transcripts in RNA-Seq: "A penalized likelihood approach for ro...
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Quantifying gene expression is usually done using RPKM. Here's another method. I still don't have any favourites, what about you?

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9 commands to check hard disk partitions and disk space on Linux

9 commands to check hard disk partitions and disk space on Linux | Bioinformatics tools | Scoop.it
Here is a quick list of 9 commands that you can use to check the partitions on hard drives and disks on your Linux system and how much space each partition has.
rougeforfire's insight:

Let's say that you are working with a massive amount of data on a distant cluster and that you want to check out the free space in your /work. Of course there are some extra bits of info to master your free space in your own computer ;-)

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2014 Millennium Technology Prize Winner Stuart Parkin - YouTube

Physicist Stuart Parkin won the 2014 Millennium Technology Prize for his pioneering contribution to the science and application of nano-magnetic material pro...
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Stuart Parkin, The father of the modern hard drive, and a pioneer of data storage

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Learning the shell - Lesson 7: Permissions

Learn the Linux command line
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Have you tried to teamwork on a lab without a server where share documents ?  Build a mini plateform by yourself and learn how to give access and permission to different users to read, write or modify files.

 

STOP FILE FORKING in a research team !

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Methods in Molecular Biology: Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes (2014)

Methods in Molecular Biology: Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes (2014) | Bioinformatics tools | Scoop.it

Genome architecture often reflects an organism’s lifestyle and can therefore provide insights into gene function, regulation, and adaptation. In several lineages of plant pathogenic fungi and oomycetes, characteristic repeat-rich and gene-sparse regions harbor pathogenicity-related genes such as effectors. In these pathogens, analysis of genome architecture has assisted the mining for novel candidate effector genes and investigations into patterns of gene regulation and evolution at the whole genome level. Here we describe a two-dimensional data binning method in R with a heatmap-style graphical output to facilitate analysis and visualization of whole genome architecture. The method is flexible, combining whole genome architecture heatmaps with scatter plots of the genomic environment of selected gene sets. This enables analysis of specific values associated with genes such as gene expression and sequence polymorphisms, according to genome architecture. This method enables the investigation of whole genome architecture and reveals local properties of genomic neighborhoods in a clear and concise manner.


Via Kamoun Lab @ TSL, Food Security
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This seems pretty interesting.. That's a nice gift idea

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BLAST - YouTube

BLAST - YouTube | Bioinformatics tools | Scoop.it
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Has it always been a pain in the ass to undersand how to interpret the results of a BLAST ?  NCBI has decided to explain it on video, Very good choice for the people who is in a hurry

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Genomic tRNA Database

Genomic tRNA Database | Bioinformatics tools | Scoop.it

This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature.


Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions (esp. due to variable post-transcriptional anticodon modification), and questionable tRNA identifications (due to pseudogenes, SINES, or other tRNA-derived elements). We attempt to document all cases we come across, and welcome feedback (lowe @soe.ucsc.edu) on new or unrecognized discrepancies. For a more detailed description of information in tables and the tRNA search algorithm, see the [Legend]. 

 

[Find tRNAs]


Via Dr. Stefan Gruenwald
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Searching for a #transcripts #database ?? why not this one ?

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On Bioinformatics and Fungal Genomics - Emacs for computational Biology - Part 1

On Bioinformatics and Fungal Genomics - Emacs for computational Biology - Part 1 | Bioinformatics tools | Scoop.it

Via Mel Melendrez-Vallard
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So you need a lab book while doing bioinformatics ? Here's one way to do it

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