Fengyuan Hu boboppie
boboppie
/ bayes_update.R
Created
August 17, 2012 16:00
— forked from cjbayesian/bayes_update.R
generate a video demonstrating Bayesian updating
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| ## Corey Chivers, 2012 ## | |
| sim_bayes<-function(p=0.5,N=100,y_lim=20,a_a=2,a_b=10,b_a=8,b_b=3) | |
| { | |
| ## Simulate outcomes in advance | |
| outcomes<-sample(1:0,N,prob=c(p,1-p),replace=TRUE) | |
| success<-cumsum(outcomes) | |
| for(frame in 1:N) | |
| { | |
| png(paste("plots/",1000+frame,".png",sep="")) |
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| #http://samtools.sourceforge.net/mpileup.shtml | |
| SAMDIR=/usr/local/package/samtools-0.1.18 | |
| SAMTOOLS=$(SAMDIR)/samtools | |
| BCFTOOLS=$(SAMDIR)/bcftools/bcftools | |
| BWA=/usr/local/package/bwa-0.6.1/bwa | |
| REF=chr22.fa | |
| .INTERMEDIATE : align.sam random_1.sai random_2.sai align.bam variations.bcf |
boboppie
/ tax_search.R
Created
September 18, 2012 06:11
Quick test of using genomes package in Bioconductor for taxonomy search
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| # genomes - Genome sequencing project metadata | |
| # URL : http://www.bioconductor.org/packages/release/bioc/html/genomes.html | |
| library(genomes) | |
| ncbiTaxonomy("human", summary=TRUE) | |
| ################################# | |
| # [1] "1 result found" | |
| # taxid name rank division nucl prot struct genome gene | |
| # 1 9606 Homo sapiens species primates 9936177 677498 20041 51 43470 |
boboppie
/ psqlfix.txt
Created
November 26, 2012 14:16
Change postgres (9.1.6) default template1 to SQL_ASCII encoding
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| fh293@newt:~$ sudo -u postgres psql | |
| psql (9.1.6) | |
| Type "help" for help. | |
| postgres=# update pg_database set datallowconn = TRUE where datname = 'template0'; | |
| UPDATE 1 | |
| postgres=# \c template0 | |
| You are now connected to database "template0" as user "postgres". | |
| template0=# update pg_database set datistemplate = FALSE where datname = 'template1'; | |
| UPDATE 1 |
boboppie
/ monte-carlo-sample.r
Created
February 7, 2013 09:34
— forked from jkeirstead/monte-carlo-sample.r
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| # Generate a Monte Carlo sample using Sobol' low-discrepancy quasi-random sequences | |
| # James Keirstead | |
| # 3 February 2012 | |
| # | |
| # Random sampling with R's standard methods is inefficient for Monte Carlo analysis as | |
| # the sampled values do not cover the parameter space evenly. This Gist allows users | |
| # to create parameter samples using Sobol' sequences to get around this problem. | |
| # makeMCSample | |
| # Makes a Monte Carlo sample using Sobol' sequences |
boboppie
/ fishlakes.csv
Created
February 22, 2013 14:17
— forked from noamross/fishlakes.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 41 columns, instead of 39. in line 2.
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| "","X","Lake.ID","Name","treatment","shorline","sizehectars","elevation","UTM.zone","northing","easting","BUBO.breeding","BUBO.breeding2","PSRE.breeding.Y.N","RACA.y.n","veg.extent","X..of.transects.with.veg","bank.slope","silt.0.1.","silt.total","X10cm.area","vegetated.area","RACA.1K","lakes.1k","dist.ave","ls","raca.basin","fish.basin","lakes.basin","co.lakes.basin","ls2","woody","herbacious","unveg","total","woodyprop","herbprop","unvegprop","logveg","archerb","arcsilt" | |
| "1",1,531,"Mill Creek",0,377.96,0.713,2008.9368,10,518882,4565085,"y",1,"n","y",0.691,0.682,0.308095216,0.6818,0.71212,111.5,261.17,3,4,0.5538,0.75,3,0,3,0,1,6082255.229,54367.17182,1399749.194,7536371.595,0.807053521,0.007213972,0.185732508,2.41692328905509,0.0850375574910141,1.00445938904933 | |
| "2",2,533,"East Boulder",1,1356.4,11.4,2034.8448,10,518069,4564441,"y",1,"y","y",2.28,0.292,0.092475736,0.376,0.3472,980.56,3092.59,5,10,0.8268,0.5,4,4,8,2,0.5,5699686.549,1302747.189,1470012.242,8472445.979,0.67273212,0.15376282,0.173505059,3.4903223 |
boboppie
/ grime_dice.R
Created
April 7, 2013 23:21
— forked from cjbayesian/grime_dice.R
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| ## Simulate Grime Dice ## | |
| red<-c(4,4,4,4,4,9) | |
| blue<-c(2,2,2,7,7,7) | |
| olive<-c(0,5,5,5,5,5) | |
| yellow<-c(3,3,3,3,8,8) | |
| magenta<-c(1,1,6,6,6,6) | |
| ## Play n match-ups between d1 and d2 |
boboppie
/ global.R
Created
June 19, 2013 08:11
— forked from dgrapov/global.R
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| #initialize | |
| library(datasets) | |
| library(ggplot2) | |
| #helper function (convert vector to named list) | |
| namel<-function (vec){ | |
| tmp<-as.list(vec) | |
| names(tmp)<-as.character(unlist(vec)) | |
| tmp | |
| } |
boboppie
/ InterMine Testing Checklist
Created
June 25, 2013 10:08
— forked from radekstepan/InterMine Testing Checklist
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| [[PageOutline]] | |
| The following items should be tested before each release. Be sure to vary the following: | |
| * super | regular user | |
| * logged in | out | |
| * Firefox, IE 7/9, Chrome, Safari | |
| * new | old user | |
| = ACCOUNT = |
boboppie
/ jarlauncher.sh
Created
August 27, 2013 10:36
— forked from stephenturner/jarlauncher.sh
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| #!/bin/bash | |
| PREFIX=$(dirname $0) | |
| java -Xmx500m -jar $PREFIX/GenomeAnalysisTK.jar $* |
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