forked from HimesGroup/BMIN503
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Module1_Optional_Reading.Rmd
172 lines (83 loc) · 6.18 KB
/
Module1_Optional_Reading.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
---
title: "BMIN503/EPID600: Module 1 Optional Reading"
output: html_document
---
***
#### Data Science
- [Data Scientist: The Sexiest Job of the 21st Century](https://hbr.org/2012/10/data-scientist-the-sexiest-job-of-the-21st-century/)
- [Data Science... Buzzword?](http://www.forbes.com/sites/gilpress/2013/08/19/data-science-whats-the-half-life-of-a-buzzword/)
- [Data Science Supply and Demand](http://www.forbes.com/sites/gilpress/2015/04/30/the-supply-and-demand-of-data-scientists-what-the-surveys-say/)
- [No-Boundary Thinking in Bioinformatics](http://www.biodatamining.org/content/6/1/19)
- [IBI faculty paper on knowledge areas needed for big data](https://www.futuremedicine.com/doi/full/10.2217/pme-2018-0145)
#### Getting Help
- [Biostars](https://www.biostars.org/)
- [Seqanswers](http://seqanswers.com/)
- [Stack Overflow](https://stackoverflow.com/)
- [How to ask questions to get help with software](http://www.catb.org/~esr/faqs/smart-questions.html)
#### Unix
- [Unix tutorial](http://www.ee.surrey.ac.uk/Teaching/Unix/)
- [Unix commands for data science](http://www.gregreda.com/2013/07/15/unix-commands-for-data-science/)
- [Unix commands for bioinformatics](http://lh3lh3.users.sourceforge.net/biounix.shtml)
#### R
- [R Manuals](https://cran.r-project.org/manuals.html)
- [R Markdown](http://rmarkdown.rstudio.com/)
- [Hadley Wickham](http://priceonomics.com/hadley-wickham-the-man-who-revolutionized-r/)
#### Git/GitHub
- [Pro Git book](https://git-scm.com/book/en/v2)
- [Intro to git and github](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004668)
- [Git guide](https://rogerdudler.github.io/git-guide/)
- [Interactive git tutorial](https://try.github.io/levels/1/challenges/1)
- [Git Magic](http://www-cs-students.stanford.edu/~blynn/gitmagic/)
- [Simple Rules for Taking Advantage of GitHub](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004947)
#### Reproducibility
- [Nature collection on challenges in irreproducible research](https://www.nature.com/collections/prbfkwmwvz)
- [Why Most Research Findings Are False](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182327/pdf/pmed.0020124.pdf)
- [Reliability of Drug Target Claims Questioned](http://blogs.nature.com/news/2011/09/reliability_of_new_drug_target.html)
- [Lies, Damned Lies, and Medical Scince](http://www.theatlantic.com/magazine/archive/2010/11/lies-damned-lies-and-medical-science/308269/)
- [Science isn't Broken](http://fivethirtyeight.com/features/science-isnt-broken/)
- [Deworming Trials](http://www.buzzfeed.com/bengoldacre/deworming-trials)
- [Reproducible Research in Computational Science](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383002/)
- [Best Practices for Scientific Computing](http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745)
- [Spurious Correlations](http://www.tylervigen.com/spurious-correlations)
- [NEJM Research Parasite Editorial](http://www.nejm.org/doi/full/10.1056/NEJMe1516564#t=article)
- [Research Parasite Award Correspondence](http://www.nature.com/ng/journal/v49/n4/full/ng.3830.html)
- [Amgen Most Pre-Clinical Studies Are not Reproducible](http://www.nature.com/news/biotech-giant-publishes-failures-to-confirm-high-profile-science-1.19269)
- [COVID-19 Models](https://science.sciencemag.org/content/368/6490/482.2)
- [COVID-19 Clinical Trials](https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2768882)
- [COVID-19 Preprints](https://www.nature.com/articles/d41586-020-01394-6)
#### Information Retrieval
- [Webscraping](https://blog.hartleybrody.com/web-scraping/)
#### Exploratory Analysis
- [Slides from Vanderbilt course on Graph Construction](http://biostat.mc.vanderbilt.edu/wiki/pub/Main/StatGraphCourse/graphscourse.pdf)
#### Visualization
- [Buzzfeed listicle format](http://www.storybench.org/using-buzzfeeds-listicle-format-tell-stories-maps-charts/)
- [rCharts Gallery](http://www.r-graph-gallery.com/all-graphs/)
- [Colorbrewer - colors for cartography](http://colorbrewer2.org/)
- [How mass breast cancer screening failed... in one chart](http://www.vox.com/2015/10/28/9631500/does-mammography-work)
- [gganimate to make animated plots in R](https://github.com/dgrtwo/gganimate)
- [Tufte style for R Markdown](http://rstudio.github.io/tufte/)
- [Causes of death visualization](http://flowingdata.com/2016/01/05/causes-of-death/)
#### Machine Learning
- [Decision Trees Visual Resource](http://www.r2d3.us/visual-intro-to-machine-learning-part-1/)
- [SVM Kernels](http://scikit-learn.org/stable/auto_examples/svm/plot_svm_kernels.html)
- [SVM Explorer](https://dash-gallery.plotly.host/dash-svm/)
- [Machine Learning Tutorial by Hastie and Tibshirani](http://www.r-bloggers.com/in-depth-introduction-to-machine-learning-in-15-hours-of-expert-videos/)
- [ROC and AUC](http://www.joyofdata.de/blog/illustrated-guide-to-roc-and-auc/)
- [How Not to Use Machine Learning: Case Study from ASHG 2015](http://andrewgelman.com/2015/10/10/gay-gene-tabloid-hype-update/)
- [Neural Net interactive demo](http://playground.tensorflow.org)
- [TensorFlow for R](https://tensorflow.rstudio.com/)
- [Connecting R to OpenML](http://openml.github.io/articles/slides/useR2017_tutorial/)
#### Data Sources
- [Lists of Goverment Data](http://www.data.gov/open-gov/)
- [Philadelphia](https://www.opendataphilly.org/)
- [LexHub, language analyses deriving insights about people](http://lexhub.org/data_sets.html)
- [A little of everything](https://github.com/caesar0301/awesome-public-datasets/blob/master/README.rst)
- [CDC Datasets](http://www.cdc.gov/nchs/data_access/ftp_data.htm)
- [Collection from Vanderbilt biostats](http://biostat.mc.vanderbilt.edu/wiki/Main/DataSets)
- [COVID-19 in Philadelphia](https://www.phila.gov/programs/coronavirus-disease-2019-covid-19/testing-and-data/)
- [COVID-19 in Delaware County](https://chesco.maps.arcgis.com/apps/opsdashboard/index.html#/fd5bfe0a9461440eb36901d61cf6b468)
- [COVID-19 in Montgomery County](https://data-montcopa.opendata.arcgis.com/pages/covid-19)
- [JHU COVID-19 Counts](https://github.com/CSSEGISandData/COVID-19)
- [NYT COVID-19 Counts](https://github.com/nytimes/covid-19-data)
- [The Atlantic COVID-19 Counts](https://covidtracking.com/about-data)
***