XenBioinfo2016

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Welcome Xenopus Bioinformatics Workshop 2016!

XenBioinfo2016 Classroom.jpg

Day 5

Day 4

  • RNAseq/MATLAB Part 2 by Virginia

Day 3

  • RNAseq by Virginia Slides
    • Dataset - /usr/local/share/xenopus/RNAseq.zip

Day 2

A = importdata('A.tab');
A.overNoise = (sum(A.data,2) > 250);
A.raw_data = A.data(A.overNoise, : );
sum(A.overNoise)
A.norm_data = A.raw_data ./ repmat( mean(A.raw_data ,2) , 1, 18) ;
[ind, c] = kmeans(A.norm_data, 24, 'dist', 'cosi', 'maxiter', 100000);
data = A.norm_data;
figure;
for i = 1:cln; subplot(4, 6, i);
whichG = (ind == i);
dd = data(whichG, :); lw = 1;
plot(dd', 'LineWidth',lw);
end

figure;hist(log(.0001 + sum(A.data,2) ), 51)   % find the noise level
A.overNoise = (sum(A.data, 2) > 12);     % create data over noise
cln=24;
[ind, c] = kmeans(A.norm_data, cln, 'maxiter', 100000,'Display','iter','dist', 'cosine' );

Day 1

See also