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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-2 votes
2 answers
129 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. ...
2 votes
0 answers
36 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 ...
1 vote
1 answer
34 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 ...
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0 votes
1 answer
50 views

replacement has 1 row, data has 0

I have tried to use UpsetR to visualize the input file which can be found here ...
2 votes
1 answer
23 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....
1 vote
2 answers
39 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 ...
0 votes
1 answer
51 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 ...
0 votes
1 answer
57 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: ...
1 vote
2 answers
70 views

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

I have multiple lists on python: ...
  • 141
1 vote
1 answer
27 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 ...
1 vote
3 answers
2k 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, ...
1 vote
1 answer
196 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 ...
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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) ...
0 votes
1 answer
199 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 ...