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Questions tagged [dataframe]

Central technical term relating to the functional method of data used in R and Python's pandas calculations

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R: How to measure mean of a column for every 10000 rows condition on other column?

I have a large bed-like dataframe with over 30 million rows. What is the best way to calculate the mean value of fourth column ...
Deb's user avatar
  • 229
3 votes
1 answer
89 views

How to calculate distance between two regions from bed like dataframe in R?

I'm wondering how can I calculate the distance between two regions from the bed (chr, start, ...
Deb's user avatar
  • 229
1 vote
2 answers
58 views

editing dataframe in r

One of the columns in my R data frame looks like this: ...
rimo's user avatar
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1 vote
1 answer
44 views

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 ...
dunc4n's user avatar
  • 35
-2 votes
2 answers
410 views

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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3 votes
0 answers
494 views

Expending UpsetR plot with Orthofinder families and gene numbers

I can create an Upset plot with the input file, which can be found here ...
user3523406's user avatar
1 vote
1 answer
126 views

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 ...
Joe_G's user avatar
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0 votes
1 answer
452 views

replacement has 1 row, data has 0

I have tried to use UpsetR to visualize the input file which can be found here ...
user3523406's user avatar
2 votes
1 answer
94 views

Turning GMT file into data frame so that third column is comma seperated

Similar to: How to convert data in gmt format to dataframe? I have downloaded a GMT file from the GSEA database (https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2022....
tacrolimus's user avatar
1 vote
2 answers
478 views

How to identify matching and unique rows across different columns in R data-frame?

I am working on a large data-frame that has 4 columns and each column has variable rows. I am trying to find unique and identical pathways between the 4 columns (each column represents a particular ...
salman1490's user avatar
0 votes
1 answer
221 views

subset from a dataframe using other dataframe in R

I have a data frame (named as df) with single column of protein IDs and other file with two columns of protein IDs (named as df1). I need to find the df IDs present in either first or second column of ...
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0 votes
1 answer
59 views

Merge/Join one data frame (X) to multiple data frames separately

Let us say that we have some data frames named S1,S2,S3... that I want to join independently by column names to dataframe X. This is how they look like: ...
salman1490's user avatar
2 votes
3 answers
128 views

How to merge multiple list into a single dataframe replacing common values with 1 -python

I have multiple lists on python: ...
Marco's user avatar
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1 vote
0 answers
41 views

Creating multiple phenotype datasets using bootstrap method "Bootstrap-samples-by-column-of-a-data-frame-in-r" for DEG analysis

I am working on a datasets and after some discussion with my group, we doubt that maybe one or more of our controls are different than the other controls. The motivation is to see if one or more ...
salman1490's user avatar
1 vote
3 answers
4k views

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, ...
HelpNeederStudent's user avatar
1 vote
1 answer
384 views

How to write multi-sequence alignment data frame as a fasta format fast

I have a data frame where the row names are the species names, and each column can either be an Amino-Acid character or "-". I wish to write it in a fasta format. Simple example of the ...
David's user avatar
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1 vote
1 answer
52 views

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) ...
Theo Jones's user avatar
0 votes
1 answer
332 views

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 ...
Cody Glickman's user avatar