Questions tagged [pandas]
Python module widely used in data science designed around database commands and calculations
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Using PANDA to infer gene regulatory networks without ppi
I'm using this tutorial (https://github.com/netZoo/netZooM/blob/master/tutorials/panda/panda.pdf) to use PANDA to infer gene regulatory networks, but without ppi values (which I've been told can be ...
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Compare in Python / PyRanges two genomic intervals to determine whether they're separate, partially overlapping, or contained
As part of a larger analysis, I need to evaluate pairs of genomic regions (regionsA and regionsB) and perform different ...
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Getting rid of duplicates in a dictionary
I have a tsv file that lists the reads and read lengths from a FASTA file but some reads are duplicated - that's just from the analysis I did previously - but I want to only take one instance of the ...
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Refactoring pandas using an iterator via chunksize
This question was also asked on Stack Overflow
Bioinformatics rationale eggNOG files can be very big and sump all available RAM for regular to medium sized desktops.
I am looking for advice on using ...
M__♦
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Tidying MEGAN Taxonomy for Python/R Analysis
I am analysing some WGS data in MEGAN and would like to do some additional analysis in Python/R
I am having trouble Tidying the Taxonomic data in a format which would be conducive to this. Originally ...
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How to get enriched pathways in the data using continous statistic measure?
I was doing pathway enrichment analysis using the below code
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How to calculate frequency of a category with respect to the value in another column?
I was trying to calculate the frequency of disease_present (yes) when smoking status is y (yes) for each group (A, B, C, D)
<...
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How to run python request for list of url's with multiple page numbers?
Hi I am trying to get the cancer ontologies (obo_id and label) from EBI-OLS. Earlier I have used the below code to get the obo_id terms and ...
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calculating mutation frequencies for every gene
I have a dataset for mutation data and I want to calculate mutation frequencies across all genes
df (This is only the small subset of data)
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Math on Pandas Columns
I have a pandas dataframe that reads in a PAF file from minimap2. What I would like to do is take the first 5 columns of the data from to create a BED file.
I used this to extract the first 5 columns:
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expansions and contractions from OrthoFinder
The input file looks like this, and the complete file can be found here:
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How to get separate histograms plots on the basis of the column value?How to detect which plot has most deviation?
I have a data frame (df) which has correlations calculated for different genes with respect to different ID combinations. I want to get separate histogram plot based on the gene name (separate plot ...
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Merge the dataframes with python iterator
I have 3 experiment files (File1.tsv, File2.tsv, File3.tsv) from three experiments and 1 library file (library_file.tsv). I want ...
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Merge data frame on either of the 2 columns in R or python
I have two data frames. One data frame with one column and second data frame with two columns. I need to merge first data frame with either column of the second data frame and returns the values. ...
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HTTP status code: 400 "Value must be an integer" error uploading JSON schema results to benchling
I am writing a benchling uploader script in python to upload data from a csv file in a JSON formatted schema to the benchling API platform. My function to create the JSON schema in the script looks ...
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How to merge multiple list into a single dataframe replacing common values with 1 -python
I have multiple lists on python:
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To create a new column with Pandas on the basis of two types of column values
I have a data frame df. The below table only represent top 8 rows of the data frame. There are multiple combination of ...
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Help to create a dataframe in Python from a FASTA file
I want to create a dataframe in Python starting from a FASTA format file. Given the toy FASTA file that I am attaching, I built this program in Python that returns four colums corresponding to id, ...
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How can I use pandas agg here to avoid iteration?
can anyone help me improve this pandas code?
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Adding multiple dataframes to compare against genotypes - DATE/LOCATION - geotemporal incidences of SARS2 genotypes
I'm trying to reuse some code I have previously used to add extra parameters.
In the initial code, it was used to give a 1/0 counter if a specific mutation was present (first code below)
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Converting hmmer --tblout to pandas dataframe [closed]
Is there a way to convert a hmmer output to a pandas dataframe? I am also unsure how to load a hmmer tblout table into python via the Bio module. I believe you can call a hmmer format with SeqIO.parse ...
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how do i change a variable with iterator under a for loop in python
This question comes up in my bioinfo class.
I have a csv file containing gene names and the cluster they belong to. I want to run GESA on each individual cluster. So I would like to extract the list ...
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Possibility to save output blastn table in memory using biopython
Is there a possibility, using biopython to save output table of blastn in memory, not in file on hard drive, for process it using pandas for example and then delete it from memory?
I mean, is there a ...
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How to load output from the kegg API in biopython into a pandas dataframe?
Biopython provides a (bit unintuitive) API to access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). I am trying to make use of it, but the output is quite unhandy as a string. What is the best ...
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How to do `bedtools intersection` using pandas alone?
I have two pandas Dataframes, using python3.x:
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