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Tagged with bioinformaticsstatistics
5 questions
2votes
1answer
172views
First order hidden Markov model with Viterbi algorithm in Java
Introduction A first order HMM (hidden Markov model) is a tuple \$(H, \Sigma, T, E, \mathbb{P})\$, where \$H = \{1, \ldots, \vert H \vert\}\$ is the set of hidden states, \$\Sigma\$ is the set of ...
- 30.2k
4votes
1answer
694views
Function to calculate the GC content variation in a sequence
I came across this BMC Genomics paper: Analysis of intra-genomic GC content homogeneity within prokaryotes And I implemented some Python functions to make this available as part of a personal project. ...
1vote
1answer
504views
Calculate and plot statistics on an R matrix
My goal is to iterate over a datamatrix, calculate mean, standard error of the mean, and then have a bar plot representing the 2 groups of my data matrix in R. My code below works as a for loop. ...
- 111
4votes
0answers
173views
Vectorize Fisher's Exact Test
I have two data frames/ lists of data, humanSplit and ratSplit, and they are of the form ...
- 141
8votes
3answers
576views
Statistical calculations with sets of genes
The following piece of code executes 20 million times each time the program is called, so I need a way to make this code as optimized as possible. ...
- 191
