Hello, I am new to bioinformatics. I am trying to make a heat map for my up and down-regulated genes for a given condition.
I want to show only up and down-regulated genes with or without showing gene names on the heat map. My gene list is 269 , so I am not sure if I can show all genes. I have cuffdiff output file and HTSeq counts. I also checked a lot of tutorials, but I could not find a code which fits my need.
I read DESeq2 documentation, but still can not make such a heat map. I have two biological replicates for each condition.
Thank you very much.
I tried to make a heatmap with bioinfokit on python from https://reneshbedre.github.io/blog/hmap.html using FPKM values from cuffdiff.
But when import my data I got error messages, which I can't solve.
This is the code on jupyter notebook
from bioinfokit import analys, visuz
df = analys.get_data('hmap.csv').data
and below is the error message.
Error: Provide correct parameter for data
AttributeError Traceback (most recent call last) <ipython-input-3-05cbc17535b8> in <module> 1 from bioinfokit import analys, visuz ----> 2 df = analys.get_data('hmap.csv').data
AttributeError: 'get_data' object has no attribute 'data'
Please help me with this error message. I would like to use this bioinfokit.
First time trying to make a post here, so it might not be very clear about what I am looking for. Thanks for your patience. Best wishes, Thanks.