User: user_without_id

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Posts by user_without_id

<prev • 26 results • page 1 of 3 • next >
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Comment: C: predicting some phenotype by gene
... Was your idea 1) to try 20'000 models one for each gene, or 2) dump all the expression of all 20'000 genes into one model? In case of 2), you have very few samples, cf. e.g. [this tutorial](https://uc-r.github.io/regularized_regression). ...
written 16 days ago by user_without_id140
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Comment: C: Recoding SNP genotype data from nitrogenous bases to 0 1 2 format
... In your [comment on SO](https://stackoverflow.com/q/63053309/) you say "checkATCG function called by recodeSNPs rejects a matrix with anything other than A T G and C", even tho the docs [say](https://www.rdocumentation.org/packages/scrime/versions/1.3.5/topics/recodeSNPs) it should work. Maybe you c ...
written 20 days ago by user_without_id140
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Answer: A: How to remove zero-length edges in newick tree
... Probably there is a slicker way... but this seems to work. #!/bin/env python3 import ete3 as ete input = "((a:1,b:1)z:0,c:1);" # http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees tree = ete.Tree(newick=input, format=1) ...
written 22 days ago by user_without_id140
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Comment: C: How to remove zero-length edges in newick tree
... the input/output is a string? ...
written 22 days ago by user_without_id140
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Answer: A: Script to obtain human protein sequences by the gene symbols
... Based on the comment by genomax. Uses [biopython](https://biopython.org/wiki/Download) to parse the Fasta file. #!/bin/env python3 import gzip import io import re import datetime from pathlib import Path from Bio import SeqIO url = "https://www.uniprot.org/ ...
written 22 days ago by user_without_id140
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Comment: C: DESeq2 of log2(count+1) transformed TCGA htseq counts from Xenabrowser
... António, would you have a reference for this? Thank you. ...
written 22 days ago by user_without_id140
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Comment: C: predicting some phenotype by gene
... And what are those groups A--D? ...
written 23 days ago by user_without_id140
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Comment: C: PRS with Plink - troubleshooting
... Is it clear that plink accepts a gz-file for `--score`? No mention in the [doc](http://www.cog-genomics.org/plink/1.9/score). Otherwise it might help to see the first few lines of the (decompressed) file. ...
written 23 days ago by user_without_id140
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Comment: C: predicting some phenotype by gene
... How many samples do you have for training the linear model, what tissue/s do they come from, is it bulk or single-cell, and how many per individual? ...
written 23 days ago by user_without_id140
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Answer: A: awk column number is a variable
... I would do something like this, in python, to filter for the columns of interest. #!/usr/bin/env python3 path_ec = "~/Downloads/GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_expected_count.gct.gz" path_sa = "~/Downloads/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt" ...
written 23 days ago by user_without_id140

Latest awards to user_without_id

Scholar 23 days ago, created an answer that has been accepted. For A: ncbi entrez protein by taxonomy ID
Scholar 24 days ago, created an answer that has been accepted. For A: ncbi entrez protein by taxonomy ID
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: ncbi entrez protein by taxonomy ID

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