QPCR | Fold Changes and Student 's t-tests from qRT-PCR experiment

 by   zqfang Python Version: Current License: No License

kandi X-RAY | QPCR Summary

kandi X-RAY | QPCR Summary

QPCR is a Python library. QPCR has no bugs, it has no vulnerabilities and it has low support. However QPCR build file is not available. You can download it from GitHub.

Two python scripts aim at calculating the Delta_Ct, Delta_Delta_Ct, Fold Changes, Student's t-test, and P-value value which produced by Quantitative real-time polymerase chain reaction (qRT-PCR).
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              QPCR has a low active ecosystem.
              It has 11 star(s) with 9 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 0 have been closed. On average issues are closed in 252 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of QPCR is current.

            kandi-Quality Quality

              QPCR has no bugs reported.

            kandi-Security Security

              QPCR has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              QPCR does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
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              Without a license, all rights are reserved, and you cannot use the library in your applications.

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              QPCR releases are not available. You will need to build from source code and install.
              QPCR has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed QPCR and discovered the below as its top functions. This is intended to give you an instant insight into QPCR implemented functionality, and help decide if they suit your requirements.
            • Main function to run the function
            • Calculate statistics for each sample
            • Calculate the Factor of a DataFrame
            • Tests two arrays
            • Creates a star
            • Reshape dataframe to csv
            • Parse input
            • Read an input file
            • Return the minimum value of an array
            • Remove outliers
            • Parse command line arguments
            Get all kandi verified functions for this library.

            QPCR Key Features

            No Key Features are available at this moment for QPCR.

            QPCR Examples and Code Snippets

            No Code Snippets are available at this moment for QPCR.

            Community Discussions

            QUESTION

            Adding hatches or patterns to ggplot bars
            Asked 2021-Apr-22 at 07:19

            Suppose I want to show in a barplot the gene expression results (logFC) based on RNA-seq and q-PCR analysis. My dataset looks like that:

            ...

            ANSWER

            Answered 2021-Apr-22 at 07:19

            Following the linked answer, it seems quite natural how to extend it to your case. In the example below, I'm using some dummy data structured like the head() data you gave, since the csv link gave me a 404.

            Source https://stackoverflow.com/questions/67164758

            QUESTION

            Pandas TypeError when trying to count NaNs in subset of dataframe column
            Asked 2021-Feb-23 at 19:05

            I'm writing a script to perform LLoD analysis for qPCR assays for my lab. I import the relevant columns from the .csv of data from the instrument using pandas.read_csv() with the usecols parameter, make a list of the unique values of RNA quantity/concentration column, and then I need to determine the detection rate / hit rate at each given concentration. If the target is detected, the result will be a number; if not, it'll be listed as "TND" or "Undetermined" or some other non-numeric string (depends on the instrument). So I wrote a function that (should) take a quantity and the dataframe of results and return the probability of detection for that quantity. However, on running the script, I get the following error:

            ...

            ANSWER

            Answered 2021-Feb-23 at 16:00

            Does the following achieve what you want? I made some assumptions on the structure of your data.

            Source https://stackoverflow.com/questions/66335912

            QUESTION

            Write text to fixed position in paragraph with iText7
            Asked 2021-Feb-12 at 14:20

            I try to write a pdf file with a header, logo and table using iText7 in c#.

            I never used iText7 before and therefore I don't know how to write text in a paragraph to a fixed position.

            Right now I am just using tabstops as anchors for my text. But the problem here is, when the string is too long everything following in the line will be shifted by a tabstop and the "columns" in the header aren't aligned anymore.

            The following picture is what I want too achieve:

            This picture shows what happens if a string gets too long (in this example I used a long username):

            Here is a code snippet I use to write one line of the header:

            ...

            ANSWER

            Answered 2021-Feb-07 at 02:49

            Instead of Tab/Tabspace use Tables and Cells so that alignment will be proper.

            Create table of column 8 size (Label, Value, space , Label, Value, Space, Label, Value)

            Use this sample Code.

            PdfPTable table = new PdfPTable(8);

            PdfPCell cell;

            cell = new PdfPCell();

            cell.setRowspan(2); //only if spanning needed

            table.addCell(cell);

            for(int aw=0;aw<8;aw++){

            table.addCell("hi");

            }

            Source https://stackoverflow.com/questions/66008312

            QUESTION

            R funtion to merge rows by id and create separate columns
            Asked 2021-Jan-13 at 10:52

            I have a list of articles obtained from an API, with my dataframe looking like this:

            ...

            ANSWER

            Answered 2021-Jan-12 at 18:35

            This is mostly a dupe from Rui's comment, but it helps to add a help-column to get it (I'll use row here). Since you started using data.table, I'll stick with that.

            Edited to work with the updated data. (I'm assuming that pmid uniquely defines the groups.)

            Source https://stackoverflow.com/questions/65687467

            QUESTION

            Substitution of rowr function
            Asked 2020-Oct-22 at 22:11

            I'm studying some projects in R and was faced with this situation

            ...

            ANSWER

            Answered 2020-Oct-22 at 22:11

            rowr was removed from CRAN, see here: https://cran.r-project.org/web/packages/rowr/index.html

            You can install an old version from the archive, to see if the code still works.

            If it doesn't, then take a look at the 'rollapply' function from the 'zoo' package, it looks very similar to what the function you presented here is doing.

            Source https://stackoverflow.com/questions/64487348

            QUESTION

            Error propagation dataframe using Montecarlo simulation
            Asked 2020-Jul-16 at 12:47

            I am doing error analysis of predictive models and I need to calculate global error, this is, I need to calculate the resultant error from propagation of indirect measurements errors. My data "df" looks like something similar to this

            Where 'x' and 'y' are the measured variables, and 'x_se' and 'y_se' the standard errors of these measurements

            I have used function 'propagate' from package 'qpcR' for the first row

            ...

            ANSWER

            Answered 2020-Jul-16 at 12:47

            This is one possible solution to obtain the res$summary for each row of your dataframe.

            You first create a custom function my_fun that does what you were trying to do for a single row of the dataframe. Then, you apply this function to each row of your dataframe. The end result would be a list with as many elements as your dataframe rows.

            Source https://stackoverflow.com/questions/62929735

            QUESTION

            Struggling with data input for R
            Asked 2020-May-21 at 19:37

            This is my first ever post so do let me know if there's anything not right or how I can improve, I am a complete novice to all this. For example, I didn't know how to make a proper table for my data so it is in bullet points.

            So I currently have a data output from running a qPCR. I have the relative expression of my gene of interest in my treatments alongside the Standard Error, 95% Confidence intervals and P(H1) probability result is due to chance.

            ...

            ANSWER

            Answered 2020-May-20 at 16:34

            You can use geom_errorbar() to plot your own confidence intervals.

            For example (bioinformatics is not my field, I'm making stuff up, sorry :D):

            Source https://stackoverflow.com/questions/61917901

            QUESTION

            kivy multiple instances of a screen with unique data
            Asked 2020-May-10 at 21:34

            good day

            is it possible to have multiple instances of a screen each using unique data? for example, i have a 'homescreen' with various buttons for various categories that takes you to a batch list screen unique to that category where you can add batches to be listed. each buttons batch list screen would have unique data to that category but the template for all batch list screens are the same.

            ive made a simple example for one category but in order to expand it to the others would i need to repeat the code and create appropriately named .kv files and add each screen to the screen manager.

            .py

            ...

            ANSWER

            Answered 2020-May-10 at 21:34

            As this is a lot of code you will have a hard time finding someone to give you a specific answer. Without looking through all of your code, yes it is possible to have multiple instances of a screen with unique data. This is exactly the use case of class instances. You simply need to pass a variable, list or object into the instance. I will give you a short example, then you should be able to figure it out yourself for your code.

            Source https://stackoverflow.com/questions/61717297

            QUESTION

            how to calculate the radius of a trajectory with given 'x' and 'y' positions in R
            Asked 2020-Feb-20 at 19:47

            I have trajectories of some moving objects in a data frame for example three trajectories were considered here as shown below:

            ...

            ANSWER

            Answered 2020-Feb-20 at 19:47

            It is not completely clear what you mean with "radius of a trajectory". Here I assume you want to fit data points of a trajectory with a circle that runs through these points. We will look at your first example.

            Source https://stackoverflow.com/questions/60320278

            QUESTION

            Specific data extraction from xml using python
            Asked 2020-Feb-14 at 17:44

            I want to collect specific information from data.xml with root[0] 'CaplockSet' contain more than 100 'Caplock' in which I need only author information to be extracted! Kindly help me with this, your support is highly appreciated.

            ...

            ANSWER

            Answered 2020-Feb-14 at 08:23

            Maybe this should work

            Source https://stackoverflow.com/questions/60221531

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install QPCR

            You can download it from GitHub.
            You can use QPCR like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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