malonzm1
malonzm1
Hi! I understand `model.forward_backward(sequence)` returns the transition probability matrix. I just wanted to clarify the order. If I had 3 hidden states (with start and end) will the row/column names...
Hi! `viterbi_likelihood, viterbi_path = model.viterbi(sequence)` returns -inf for viterbi_likelihood and an empty viterbi_path. Below is the code. For a different dataset it worked. [total_reads_Y.txt.tar.gz](https://github.com/jmschrei/pomegranate/files/8867428/total_reads_Y.txt.tar.gz) [methylated_reads_Y.txt.tar.gz](https://github.com/jmschrei/pomegranate/files/8867435/methylated_reads_Y.txt.tar.gz) ``` import numpy as np...
When I try to run this code, `model = HiddenMarkovModel.from_samples(MultivariateGaussianDistribution, n_components=5, X=diffs, n_jobs=4)` it returns a Segmentation fault. Pls. advise. Thanks and good day.
Can I fix the gaussian means for the clusters in HMM? (I'm not sure if this is the right space for this question but I don't know any other forum...
Hi! Is there a way to find the state probabilities for each step in the sequence? Thanks and good day.
Hi, I have datasets that I need to concatenate. Is it ok to run celltypist after concatenation or should I run it on the individual datasets before concatenation? Thanks and...
Hi, In issue https://github.com/MaayanLab/archs4/issues/30, you shared how to obtain gene abundance values from the transcript expression levels. I would like to know how to obtain CPM and TPM values from...
Hi, When I use the R script (h5read(destination_file, "meta/genes/gene_symbol")) the matrix generated includes genes with prefix ENSG along with regular gene symbols. Why is this? Thanks and good day.
Hi again, When I upload a fastq.gz file to elysium from a server (tunneled via SMB), I get the following error: RequestTimeoutYour socket connection to the server was not read...
Hi, Why are the gene counts from elysium in float format whereas the gene counts from archs4 in integer? Thanks.