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matplotlib | |
numpy==1.26.4 | |
pandas | |
scanpy | |
scikit_learn | |
scipy | |
plotnine | |
seaborn | |
jupyterlab | |
Cython |
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function mmwrite(filename,A) | |
mmfile = fopen(filename,'w'); | |
[M,N] = size(A); | |
[I,J,V] = find(A); | |
NZ = length(V); | |
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#!/bin/bash | |
bcftools view -H input.vcf.gz | \ | |
awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6 "\t" $7 "\t" $8 "\t" $9 "\t" "0/1"}' | \ | |
cat <(bcftools view -h -s SOME_SAMPLE input.vcf.gz) - | \ | |
bgzip > \ | |
output.vcf.gz | |
bcftools view -H output.vcf.gz | awk '{ print $1 "\t" $2 - 1 "\t" $2 }' | bgzip > output.bed.gz |
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import pyro | |
from pyro.infer import SVI, Trace_ELBO, TraceEnum_ELBO, config_enumerate | |
from torch.distributions import constraints | |
data = 2. * torch.Tensor( [-1., -0.5, -0.5, .5, .8, 1.] ) | |
def model(data): | |
guide_efficacy = pyro.sample('guide_efficacy', dist.Beta(1., 1.).expand([len(data)]).to_event(1) ) | |
gene_essentiality = pyro.sample("gene_essentiality", dist.Normal(0., 5.)) | |
mean = gene_essentiality * guide_efficacy |
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require(VariantAnnotation) | |
require(GenomicRanges) | |
get_cis_geno = function(tab, chrom, left, right, genome_build = "GRCh38") { | |
gr = GRanges(chrom, IRanges(left, right)) | |
sp = ScanVcfParam(which = gr) | |
vcf = readVcf(tab, genome_build, param = sp) | |
gt = geno(vcf)$GT | |
if (nrow(gt) == 0) return(NULL) | |
allele1 = substr(gt, 1, 1) |
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#' Consistent implementation of diag | |
fix_diag=function(x) { | |
if(length(x)==1) matrix(x) else diag(x) | |
} | |
unscale = function(x) { | |
x = sweep(x, 1, attr(x, "scaled:scale"), "*") | |
sweep(x, 1, attr(x, "scaled:center"), "+") | |
} |
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def pixel_shuffle_1d(x, upscale_factor): | |
batch_size, channels, steps = x.size() | |
channels //= upscale_factor | |
input_view = x.contiguous().view(batch_size, channels, upscale_factor, steps) | |
shuffle_out = input_view.permute(0, 1, 3, 2).contiguous() | |
return shuffle_out.view(batch_size, channels, steps * upscale_factor) |
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#!/bin/bash | |
set -e | |
outfile=$2 | |
if [ "$#" -eq 1 ]; then | |
outfile=$1 | |
fi | |
gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dSAFER -dCompatibilityLevel=1.5 -sOutputFile=temp.pdf $1 | |
# so you can run on the same file | |
mv temp.pdf $outfile |
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library(ggplot2) ## devtools::install_github("hadley/ggplot2) | |
library(grid) ## rasterGrob | |
library(EBImage) ## readImage | |
library(ggthemes) ## theme_minimal | |
## ########## | |
## INDEPENDENT CODE TO BE SOURCED: | |
## ########## | |
# user-level interface to the element grob |