gtex | GTEx analysis scripts

by hall-lab Python Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | gtex Summary

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

GTEx analysis scripts

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Quality

Security

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Support

gtex has a low active ecosystem.

It has 16 star(s) with 9 fork(s). There are 6 watchers for this library.

It had no major release in the last 6 months.

gtex has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of gtex is current.

Quality

gtex has 0 bugs and 0 code smells.

Security

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

gtex code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

gtex does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

gtex releases are not available. You will need to build from source code and install.

gtex has no build file. You will be need to create the build yourself to build the component from source.

It has 3376 lines of code, 171 functions and 31 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed gtex and discovered the below as its top functions. This is intended to give you an instant insight into gtex implemented functionality, and help decide if they suit your requirements.

Normalize expression and counts
Normalize quantiles
Inverse of inverse quantile normalization
Convert GTF file to BED
Extract the contributors from a vcf file
Read a GCT file from a GCT file
Write a BED file to a tabix file

Get all kandi verified functions for this library.

gtex Key Features

No Key Features are available at this moment for gtex.

gtex Examples and Code Snippets

No Code Snippets are available at this moment for gtex.

Community Discussions

Trending Discussions on gtex

Extracting elements from a nested list to a data.matrix

merge two datasets based on common column

edit row and columns in R

edit sampleID info in vcf file

R: Error says invalid 'type' (character) of argument

Counting two tables with several conditions

Which element is the most frecuent according to a second table

Combine table data in MySQL using JOIN

How do I sort by a new generated column in mySQL?

How to get a unique output file for each loop with bash

QUESTION

Extracting elements from a nested list to a data.matrix

Asked 2022-Feb-24 at 19:26

I have a list of 2 elements that each has 3 elements. In every 3 elements, there is a list of length 2 nested elements so that each includes a tibble with rows and columns. tibbles' dimension is fixed for rows but the columns are different from the third column.

Here is the structure:

...

ANSWER

Answered 2022-Feb-24 at 19:26

As it is nested, an option is rrapply

Source https://stackoverflow.com/questions/71257015

QUESTION

merge two datasets based on common column

Asked 2022-Feb-23 at 14:07

I have one question. Like now i have two files:sampleattributes and genecount.I have filtered sample attributes file and it has a column name sampid and genecount has a column name sampid. I am trying to merge the two files using the common sampid. This is what I have written:

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ANSWER

Answered 2022-Feb-23 at 14:07

Looking at youre gene_count data, it doesn't have a column for the SAMPID, those were imported as row names. We'll convert them to an actual column, replace the "." with "-" so they match the braindata format, and then we can join. Your sample data doesn't have any elements in common so I use a full_join, but you may prefer a left, right, or inner join--I'm not really sure what your use case is.

Source https://stackoverflow.com/questions/71213949

QUESTION

edit row and columns in R

Asked 2022-Feb-20 at 18:55

I want to do this: Input:

For the output i want to have the GTEX id as rows and ENSG as columns. Like this:

SAMPLEID ENSGO ENSGO ENSGO
GTEX-1117F-022~ 0 187 0
GTEX-1117F-042~ 0 109 0

I tried to do this command but it doesn't give me the correct output:

...

ANSWER

Answered 2022-Feb-20 at 18:55

With base R

Source https://stackoverflow.com/questions/71190289

QUESTION

edit sampleID info in vcf file

Asked 2022-Feb-14 at 22:33

I have a vcf file whose header has sample ID info. It looks like this:

##fileformat=VCFv4.2 ##FILTER= ##fileDate=20220214 ##source=PLINKv1.90 ##contig= ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GTEX-1117F_GTEX-1117F GTEX-111CU_GTEX-111CU GTEX-111FC_GTEX-111FC GTEX-111VG_GTEX-111VG GTEX-111YS_GTEX-111YS GTEX-1122O_GTEX-1122O GTEX-1128S_GTEX-1128S GTEX-113IC_GTEX-113IC GTEX-113JC_GTEX-113JC GTEX-117XS_GTEX-117XS

I want to edit it to contain only

##fileformat=VCFv4.2 ##FILTER= ##fileDate=20220214 ##source=PLINKv1.90 ##contig= ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GTEX-1117F GTEX-111CU GTEX-111FC GTEX-111VG GTEX-111YS
GTEX-1122O GTEX-1128S GTEX-113IC GTEX-113JC GTEX-117XS

Basically I want to remove anything coming after _ For example: ID:GTEX-1117F_GTEX-1117F desired ID: GTEX-1117F

I used this command but its not really giving me the desired output.

...

ANSWER

Answered 2022-Feb-14 at 22:33

Using sed

Source https://stackoverflow.com/questions/71117464

QUESTION

R: Error says invalid 'type' (character) of argument

Asked 2021-Jan-31 at 11:13

I am new to R and I am trying to view gene expression differences between tumour vs normal using a TCGA.GTEX dataset. I am trying to find the log fold change for all columns.

This is the code I applied:

...

ANSWER

Answered 2021-Jan-30 at 21:14

It seems to me some columns in TCGA_GTEX_lung[-7] are character. You need numeric to calculate sum. You can check this with code apply(df, 2, function(x) class(x)). If this is the case, you can convert character to numeric with as.numeric().

Edit

Source https://stackoverflow.com/questions/65971895

QUESTION

Counting two tables with several conditions

Asked 2020-Dec-19 at 00:28

I have two tables,

fenotipos

...

ANSWER

Answered 2020-Dec-19 at 00:28

You could do:

Source https://stackoverflow.com/questions/65365540

QUESTION

Which element is the most frecuent according to a second table

Asked 2020-Dec-18 at 23:41

I have two tables,

phenotipos

...

ANSWER

Answered 2020-Dec-18 at 22:07

You can use a correlated subquery a string functions to count how many attributes start with each phenotype:

Source https://stackoverflow.com/questions/65364508

QUESTION

Combine table data in MySQL using JOIN

Asked 2020-Dec-15 at 10:22

I'm trying to join two tables in MySQL, in one I have a set of IDs (of the type GTEX-14BMU-1526-SM-5TDE6) and a set of type's of tissue(SMTS), I have to select the IDs for the tissue type 'Blood' (which is another column of the same table), and then I have to take only the first two strings (GTEX-14BMU) from the ID name and make a list of the different ones.

Then I have to compare this to a second table in which I have a list of IDs that already are in the type (GTEX-14BMU) which have to meet the condition that the column sex of this same table is 2.

The expected result is a list with the IDs which are sex type 2 and have tissue type 'Blood', meaning the ones that are coinciding. I'm trying to solve this by using JOIN and all the needed conditions in the same statement, which is:

...

ANSWER

Answered 2020-Dec-15 at 10:17

Here:

Source https://stackoverflow.com/questions/65303864

QUESTION

How do I sort by a new generated column in mySQL?

Asked 2020-Dec-14 at 22:11

I have to sort some information that is encoded in the following form: GTEX-VJYA-2126-SM-4KL1O I have a list of this IDs and I have to take the first two strings separated by '-' (so,GTEX-VUSG) and count how many of each distinct ID I end up with.

I'm using the following MySQL code:

...

ANSWER

Answered 2020-Dec-14 at 21:59

Just repeat the expression in the ORDER BY clause:

Source https://stackoverflow.com/questions/65297077

QUESTION

How to get a unique output file for each loop with bash

Asked 2020-Aug-04 at 06:41

I have a script below, I am looping throught GTEx brain tissues and running a program laid out below. How do I in the --output put a unique output file? I am lost on this, still kind of new to bash. BTW, TISSUE files look like this: Brain_Frontal_Cortex_BA9.genes.annot and Lung.genes.annot In the GTExV8 folder, I have 48 unique files that TISSUE will loop through. Thus, the output for one example would be Brain_Frontal_Cortex_BA9_emagma and Lung_emagma

...

ANSWER

Answered 2020-Aug-04 at 05:42

No sure what you mean, but if your intention is to generate different names for the --out files based on the $tissue file name, and assuming BA9 is the variable part and you want to name the output after it, you can do

Source https://stackoverflow.com/questions/63240714

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

Vulnerabilities

No vulnerabilities reported

Install gtex

You can download it from GitHub.
You can use gtex 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.

Support

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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