padua | Proteomic Data Analysis with Python
kandi X-RAY | padua Summary
kandi X-RAY | padua Summary
The goal is to provide a simple scripting approach to replicate many of the common steps for interacting with the output of MaxQuant. Many of the steps implemented are based on similar steps used in the MaxQuant sister software Perseus. While currently Perseus has more features, it has stability issues with the larger datasets we are currently using. Having the processing steps implemented in Python allows for simple processing workflow scripts to be created and re-used.
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Top functions reviewed by kandi - BETA
- Plots a scatter plot
- Calculate s0 curve
- Build a combined label from the given list of indices
- Get shortstr from a string
- Plot rank intensity
- Generate an enrichment for a given protein sequence
- Get the protein ID from a string
- Find the index of the closest value in the array
- Cluster a DataFrame
- Cluster a dataframe
- Cluster clusters using fcluster
- Plot a box plot
- Folds the columns of a DataFrame
- Remove rows from the dataframe
- Remove contaminant contaminant contaminant
- Get a list of protein IDs from a DataFrame
- Write a hdf5 file to a file
- Takes a pandas DataFrame and a pandas dataframe
- Compares two DataFrames
- Build an index from a design matrix
- Plots the difference between two DataFrames
- Plot venn diagram
- Write phonopath ratio
- Compute a hierarchical hierarchical timecourse clustering
- Compute the KEGG for a pathway
- Remove only identified by site
padua Key Features
padua Examples and Code Snippets
Community Discussions
Trending Discussions on padua
QUESTION
In my django template I want to access the bio prop of an instance of my Creator class. This bio is set up as a QuillField in the Creator model class. When I try to access creator.bio, all that renders to the page is the following:
What I want is the actual paragraph of formatted text (ie. the bio) that I typed into the form and saved. As of now, the QuillField is only accessible through the form in the Django admin page. The problem has nothing to do with the Quill UI, but rather being able to access the text I wrote into that form field and render it to the page in a readable format.
From models.py:
...ANSWER
Answered 2021-Feb-02 at 02:57Based on https://github.com/LeeHanYeong/django-quill-editor/issues/12 it sounds like you need to use:
QUESTION
I'm trying to do a chloropeth map following this guide: https://www.r-graph-gallery.com/327-chloropleth-map-from-geojson-with-ggplot2.html
I mixed a bit of the tutorial with this answer(Chloropleth map with geojson and ggplot2), since I wasn't getting the result I expected. The cities were being filled with the same color, and it seemed as R wasn't understanding the data as numeric, and filled every city that had at least 1 user with the default color. (tried using as.numeric, didnt work either)
I downloaded "users by city" data from my website from Google Analytics using
...ANSWER
Answered 2020-Jan-28 at 22:09It looks like you have a couple relatively large values, while most are small. This causes 'skewing' of your color scale in a way that looks less interesting. Instead of graphing number of users, consider mapping based on a quantile .
Here is an implementation of grouping into quantiles using cut2() from Hmisc. In this case, values are cut into 5 groups.
QUESTION
In Python3, I need to scrape a site that has search options in bar menu: http://www.cnj.jus.br/bnmp/#/pesquisar
I just need to select the item "Estado" and within it the option "Rio de Janeiro" (it is a State of Brazil, with several cities). Then click "Pesquisar"
The site generates a screen with the items I need to store in a dataframe after (on multiple pages, with a table in each) - 53,022 items such as:
...ANSWER
Answered 2018-Apr-12 at 20:22I was able to see the right XHR request file with chrome's developer tools networks tab. I had the preserve log option checked, so that may be why I was able to see it when you weren't.
I found it by starting at http://www.cnj.jus.br/bnmp/#/pesquisar, then selecting an estado, clicking Pesquisar and then checking the network logs.
It looks like you need to make a post request to http://www.cnj.jus.br/bnmp/rest/pesquisar. Youll also need to edit the payload to include the state and the page you need.
so it should look like this:
QUESTION
I'm writing a facebook insights connector to use in google data studio but i cannot find the right way to process the response when using the metric page_fans_city in the request. The returned data has the following format:
...ANSWER
Answered 2017-Dec-14 at 19:22Your response should look more like this:
QUESTION
I have comma corrupt csv file that can be read by microsoft excel file, but can't be read well using pandas dataframe, I got macro solution, but I want solution that works in python as well, here's first 5 lines of my data
...ANSWER
Answered 2017-Sep-27 at 16:06To convert the list representations used in some of the cells:
QUESTION
I am trying to run a tutorial for prophet, which uses R magic in a Jupyter notebook. The following code:
...ANSWER
Answered 2017-Sep-16 at 18:42Many questions in the question. Answering one of them:
How do I know the location of the R kernel used by R magic in this Jupyter notebook?
In Jupyter, do:
QUESTION
All -
I recently had a box at work patched (RHEL 6.8) and it updated my version of R from 3.3.3 to 3.4.0. No biggie this happens - the only complication is that I have to go back and install packages that I need under the new version. One package I rely on is the tm.plugin.webmining package.
One of my jobs was failing and when I ran that manually I got a bunch of garbage back about that package, so I figured it was something messed up so I attempted to reinstall it, but I keep getting errors.
I've considered rolling back a version of R, but that would require a bunch of work and I really would like to move forward with the new version. Here is the console output of my R session when trying to install the package:
...ANSWER
Answered 2017-Aug-30 at 02:05After installing 3.4.1, the tm.plugin.webmining package still had issues installing, so I ended up writing my own function using base package dependencies for my needs. Just want d to post an update....
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
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Install padua
io for reading and writing both MaxQuant and Perseus format files (input/output)
filters for filtering data by quality and features
process incorporating experimental design, labels to index, expand-side-table (Perseus) and more
normalization for performing normalisation methods, e.g. remove column median
annotations adding annotation metadata for quantified proteins
analysis performing simple analyses, e.g. column correlations
plots standard plot outputs for overviews of data
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