protein clusters scaffold

Documentation about protein clusters and how they are computed in scaffold

https://proteome-software.wikispaces.com/file/view/scaffold_protein_grouping_clustering.pdf
https://proteome-software.wikispaces.com/file/view/Clustering_poster_ASMS_2013.pdf

GLM

Generalized linear models

University of Cambridge  GLM course
http://www.statslab.cam.ac.uk/~pat/

http://www.statslab.cam.ac.uk/~pat/All.pdf  (covers material in Chapter 3 in depth)

Princeton lecture notes on GLM's
http://data.princeton.edu/wws509/notes
http://data.princeton.edu/wws509/notes/a2.pdf (Chapter 3 in brief)

University of Vienna GLM course
http://statmath.wu.ac.at/courses/heather_turner/ (with R code examples)

How are the likelihood ratio, Wald, and Lagrange multiplier (score) tests different and/or similar?

http://www.ats.ucla.edu/stat/mult_pkg/faq/general/nested_tests.htm

on binomial and quasibinomial
http://stats.stackexchange.com/questions/91724/what-is-quasi-binomial-distribution-in-the-context-of-glm

Lecture videos of the university of Sheffield.

https://www.youtube.com/playlist?list=PLPmy3Mr9LPPtQF-LeU_0hrhhrpBJ-wKmI

Mixed Linear Models

http://rpsychologist.com/r-guide-longitudinal-lme-lmer

Mixed effect modelling with R book by Bates

http://lme4.r-forge.r-project.org/book/

http://lme4.r-forge.r-project.org/

Stronger together

https://www.youtube.com/watch?v=w-iuPeMdprQ

Fingers crossed.

Go links

https://github.com/ardanlabs/gotraining

Todd — Instructor · 2 months ago  Answer 

https://goo.gl/PHKgO7

PRESENTATIONS

https://goo.gl/Tbz6Xf

GITHUB CODE

https://goo.gl/KbUroF

COURSE OUTLINE

https://goo.gl/qwoSft

Mark as helpful

Math and Stats Videos

Quadratic forms

https://www.youtube.com/watch?v=LGTInfHChzA

Linear Algebra
https://www.youtube.com/playlist?list=PLflMyS1QOtxwiN5oOuyY4W_8fZlTTnRcF

Analysis of discrete data
https://www.youtube.com/playlist?list=PLflMyS1QOtxy_mfqNWpH6hWc7lqgSfKZM

Brian Caffo Playlists

https://www.youtube.com/user/bcaffo/playlists

In-depth introduction to machine learning in 15 hours of expert videos

http://www.dataschool.io/15-hours-of-expert-machine-learning-videos/

1) Functions (see in particular videos 5 and 6 on binomial expansions and 9 and 10 on exponentials and logarithms)
https://www.youtube.com/watch?v=71CUgRQIZBk&list=PLqvhP6807i-24xFjmato7ifntuu1G8-ym

2) Differentiation (also includes some material on series: see video 13.0 for arithmetic and geometric series)
https://www.youtube.com/watch?v=Yl-Mi00i8SI&list=PLqvhP6807i-1OJUwEcAtkXwFbvhlczhHd

3) Complex numbers
https://www.youtube.com/watch?v=mWrUbcrGlPs&list=PLqvhP6807i-2wtG-7l-FDEsi5eVWuMtUY

4) Vectors
https://www.youtube.com/watch?v=wbCxkf3jJ3w&list=PLqvhP6807i-0zX27olqR5MyY4uBhNkYZj

5) Integration (includes material on useful algebraic manipulation topics such as partial fractions and completing the square)
https://www.youtube.com/watch?v=elFqHzOAlzs&list=PLqvhP6807i-0nC5hcCqteLVuVOLPw6f-a

6) Matrices (includes an introduction, and sections on matrix multiplication, determinants, inverses, systems of linear equations and eigenvalues and eigenvectors)
https://www.youtube.com/watch?v=RQGD9S2C2tE&list=PLqvhP6807i-2cb7PeI1QQkHHfU-BnzZrQ

21st-centurys-100-greatest-films

21st century's 100 greatest films
http://www.bbc.com/culture/story/20160819-the-21st-centurys-100-greatest-films

greatest-comedies-of-all-time
http://www.bbc.com/culture/story/20170821-the-100-greatest-comedies-of-all-time

Best 10 movies of 2016
http://www.bbc.com/culture/story/20161215-the-10-best-films-of-2016

slow cooker recipes
http://www.bbcgoodfood.com/howto/guide/family-slow-cooker-recipes-0

shiny

Changing UI.
http://shiny.rstudio.com/articles/dynamic-ui.html

Having a run button.
http://shiny.rstudio.com/articles/action-buttons.html

Since R is single threaded the UI will block for longer running jobs:

But there is async progress bar:

http://shiny.rstudio.com/articles/progress.html

Analyzing short time series

better than pca : http://bioconductor.org/packages/release/bioc/html/made4.html
pvals  for clusters : https://cran.r-project.org/web/packages/pvclust/index.html
icc : https://cran.r-project.org/web/packages/ICC/index.html


Comparison of short time series:
https://bioconductor.org/packages/release/bioc/html/maSigPro.html


OPLS
https://www.r-bloggers.com/evaluation-of-orthogonal-signal-correction-for-pls-modeling-osc-pls-and-opls/


STEM short ts expression miner
http://www.sb.cs.cmu.edu/stem/

Software for the analysis of time-series gene expression data

http://www.nature.com/nrg/journal/v13/n8/fig_tab/nrg3244_T1.html

Working with docker

docker run -p 8888:8888 -p 6006:6006 -v /home/yourhome/notebook:/notebook b.gcr.io/tensorflow/tensorflow sh -c "jupyter notebook /notebook"



for more details see:
http://stackoverflow.com/questions/33636925/how-do-i-start-tensorflow-docker-jupyter-notebook

https://docs.docker.com/engine/getstarted/step_four/

MOOCS

MOOC platforms :

https://www.coursera.org/

https://www.edx.org/

https://www.datacamp.com/

https://lagunita.stanford.edu

https://www.udacity.com

https://www.futurelearn.com

https://www.udemy.com

http://www.dataschool.io/

http://www.statistics.com/

I did take courses on coursera, edx and udemy and some on udacity. I quite like coursera and edx because most of the courses have a very high standard, are very mature platforms providing good learning support (progress report, certificates, exercises, quizzes). I very much liked the peer review process on Coursera but haven't seen it used anymore recently.
Udemy and also Udacity are both a bit of a surprise box (some courses are great some less so) so check the user reviews.

Syria refugee crisis - how to help

If you feel the urge because of compassion to do something for the victims of the Syrian War, for the refugees in Syria and from Syria in Greece, Lebanon, Turkey etc. here are a few links you might find useful:

Refugees Welcome:
http://www.refugees-welcome.net/

RED CROSS
https://www.icrc.org/en/support-us/operations/syria-appeal

UNHC
http://donate.unhcr.org/international/syria

See Watch
http://sea-watch.org/en/

Life rescue in Lesbos Greece
http://en.proactivaopenarms.org/

Refugies in the News:

Why British surgeon cannot forget this girl

http://www.bbc.com/news/world-middle-east-38514428

Migration to Europe explained in seven charts
http://www.bbc.com/news/world-europe-34131911


Child work in Lebanon
http://www.spiegel.de/politik/ausland/fluechtlinge-kinderarbeiter-aus-syrien-schuften-im-libanon-a-1093837.html

Video of bloodied five-year-old in Aleppo
http://www.abc.net.au/news/2016-08-18/children-continue-to-pay-price-of-syria-conflict/7761322

Broad picture

Watchers of the sky documentary:
https://en.wikipedia.org/wiki/Watchers_of_the_Sky

Germany hate crime: Nearly 10 attacks a day on migrants in 2016
http://www.bbc.com/news/world-europe-39096833


07.03.2017
SYRIAN CHILDREN FACE GROWING MENTAL HEALTH CRISIS, NEW REPORT REVEALS
https://www.savethechildren.net/article/syrian-children-face-growing-mental-health-crisis-new-report-reveals

fdr

# Scaffold protein filtering:


# Peptides 1

Protein Threshold 1.0% FDR
Peptide Threshold 0.1% FDR