Questions tagged [bioinformatics]
For programming-related questions related to Bioinformatics. Other questions do not belong here, but might be on-topic at https://bioinformatics.stackexchange.com/.
bioinformatics
4,442
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dispersion.cutoff and mean.cutoff don't seem to work at all with FindVariableFeatures()
I'm doing spatial single-cell analysis on CosMx databases and I've run into a problem when using FindVariableFeatures(). I have only 960 genes in total so I wanted to plot the variable genes and ...
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4
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Error in connection querying MotifDb in R
I don't understand why some days ago this line was working
MotifDb [grep ('TWIST1', values (MotifDb)$geneSymbol, ignore.case=TRUE)]
Hsapiens_TWIST1 <- query(MotifDb, "TWIST1")
while now ...
- 637
1
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1
answer
28
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Printing residues in a selection in Pymol?
I am currently working on a protein where I have selected residues within 10A of its bound ligand in pymol. However, I can not find a way to print out what residues are contained in that group of ...
1
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2
answers
42
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What is the easiest way in Biopython to duplicate or "clone" a chain in a PDB file?
Like, say I have a PDB file with one chain (call it A for simplicity), and a symmetry matrix that sends it to a dimer partner and/or another molecule in an asymmetric unit. I want to now make one ...
- 152
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11
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TaskRun failed to finish due to an error for Coretex BioInformatics workflow
After starting bioinformatics workflow in Coretex, I am getting the following message even though data seems to be in order:
"Failed to determine which column contains sampleIDs/names..." ...
- 1
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27
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Difficulty in loading the expression data from Geodata [closed]
I'm new to Bioinformatics and have been stuck on this since last week. The problem is that I can't load up the expression data and have tried everything possible. The accession ID of this data is &...
- 3
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1
answer
18
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Multiple variables in input and output using wildcards snakemake
rule all:
input:
expand("tissues/{id}/atac_seq/{srr}/{srr}_S1_L001_R1_001.fastq.gz", id =IDs, srr = df[df['library_type']=='Chromatin Accessibility']['Library']),
expand("...
- 45
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1
answer
30
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Failed to load expression data from Geodataset in R
I'm new to Bioinformatics and have been stuck on this since last week. The problem is that I can't load up the expression data and have tried everything possible. The accession ID of this data is &...
- 3
1
vote
1
answer
21
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How to enable "output" to detect variables in "run" in snakemake
I am trying to make directories for the different "IDs" I have stored in the .csv file (they are stored under column "ID"). However, snakemake doesn't seem to be able to detect &...
- 45
3
votes
1
answer
41
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How can I import cytoscape library and use it in javascript file written in in Visual Studio Code
I want to use the cytoscape library to visualize a protein-protein interaction network. I have already installed the node.js as well as the npm. However when I run this line (import cytoscape from '...
- 31
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1
answer
56
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Not getting any output even though there are no errors [closed]
from Bio import SeqIO
from Bio import Seq
count = 0
sequence = []
for seq_record in SeqIO.parse(r"C:...\\drosophila.csv", 'fasta'):
if (count < 6):
sequence.append(...
1
vote
1
answer
5k
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How to select files in subdirectories by name and move all files containing "XXX" and "YYY" into new directories
Hello all, how can I move all files with the name "ATAC" and all files with the name "RNA" into separate folders? The context is that in the current the directory, I have many ...
- 45
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0
answers
59
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Subsequences of peptide containing more than 80 amino acids, convert output to fasta format [closed]
I have some protein sequences and I want to obtain all the possible subsequences of each one of them, containing 80 amino acids. The order of the amino acids should remain the same, I just want to ...
- 63
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12
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How to obtain the names, transcription start and end of immunoglobulin genes from mouse mm10 reference genome using ucsc?
I am new here and in the bioinformatics world, please, be kind(:
I am currently trying to obtain a list with the names, the chromosome position (or transcription start and end) of all the ...
-1
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1
answer
28
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Is there a way to make two scatter density plots share the same legend in R
I am using geom_pointdensity() to draw scatter density plot in R. Is there a way to draw them side by side as subplots and also share the same legend with the same range?
- 35