User:Jarle Pahr/Data analysis

Notes on tools and techniques for data analysis:

http://source.mozillaopennews.org/en-US/learning/statistically-sound-data-journalism/

Single value decomposition (SVD): http://en.wikipedia.org/wiki/Singular_value_decomposition

Prinicipal component analysis (PCA):

Learn Data Science: http://nborwankar.github.io/LearnDataScience/

Uniform, optimal signal processing of mapped deep-sequencing data: http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2596.html

http://datasciencemasters.org/

Software

http://brenocon.com/blog/2009/02/comparison-of-data-analysis-packages-r-matlab-scipy-excel-sas-spss-stata/

KNIME: http://www.knime.org/

Visualisation:

LookSeq: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775587/

DNA subway: http://dnasubway.iplantcollaborative.org/

Distance metrics

http://liorpachter.wordpress.com/2014/01/19/why-do-you-look-at-the-speck-in-your-sisters-quilt-plot-and-pay-no-attention-to-the-plank-in-your-own-heat-map/

Clustering

K-means

http://arxiv.org/ftp/cs/papers/0603/0603120.pdf

http://www.aaai.org/Papers/IJCAI/2007/IJCAI07-447.pdf

Bibliography

Unraveling genomic variation from next generation sequencing data: http://www.biodatamining.org/content/6/1/13