celseq2 | Generate the UMI count matrix from CEL-Seq2 sequencing data | Genomics library

by yanailab Python Version: v0.5.3 License: BSD-3-Clause

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

kandi X-RAY | celseq2 Summary

celseq2 is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. celseq2 has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

This is celseq2, a Python framework for generating the UMI count matrix from CEL-Seq2 [*] sequencing data. We believe data digestion should be automated, and it should be done in a manner not just computational efficient, but also user-friendly and developer-friendly.

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Support

celseq2 has a low active ecosystem.

It has 10 star(s) with 8 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 22 have been closed. On average issues are closed in 93 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of celseq2 is v0.5.3

Quality

celseq2 has 0 bugs and 0 code smells.

Security

celseq2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

celseq2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

celseq2 is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

celseq2 releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed celseq2 and discovered the below as its top functions. This is intended to give you an instant insight into celseq2 implemented functionality, and help decide if they suit your requirements.

Demultiplexing reads
Return a filehandle for gzipped fastq files
Create a directory
Print a message to stderr
Generate a dummy GTF
Return a string representation of a GTF file
Return a GTF attribute string
Plot a quantile count matrix
Return the base name of a file
Convert cif2 pipeline to pipeline
Get counts of bc_has reads from bc_index
Create dummy fasta file
Write demultiplexing stats
Demultiplexing a sam file
Read bc_index from bc_index file
Demultiplex a sam file
Convert a string to a list of integers
Entry point for export_snake
Create an annotation model from a GFF file
Create a new configuration file
Plotly demultiplexing stats
Plotly alignly alignment stats
Return an argument parser
Create dummy cell barcodes
Plot STU count matrix
Count the number of reads in a sam file

Get all kandi verified functions for this library.

celseq2 Key Features

No Key Features are available at this moment for celseq2.

celseq2 Examples and Code Snippets

No Code Snippets are available at this moment for celseq2.

Community Discussions

Trending Discussions on Genomics

search for regex match between two files using python

Is there a way to permute inside using to variables in bash?

BigQuery Regex to extract string between two substrings

how to stop letter repeating itself python

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Delete specific letter in a FASTA sequence

How to get the words within the first single quote in r using regex?

Does Apache Spark 3 support GPU usage for Spark RDDs?

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Usage of compression IO functions in apache arrow

QUESTION

search for regex match between two files using python

Asked 2022-Apr-09 at 00:49

I´m working with two text files that look like this: File 1

...

ANSWER

Answered 2022-Apr-09 at 00:49

Perhaps you are after this?

Source https://stackoverflow.com/questions/71789818

QUESTION

Is there a way to permute inside using to variables in bash?

Asked 2021-Dec-09 at 23:50

I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

Input files: Highland.ped - Midland.ped - Lowland.ped
Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

The general code is:

...

ANSWER

Answered 2021-Dec-09 at 23:50

Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

Source https://stackoverflow.com/questions/70298074

QUESTION

BigQuery Regex to extract string between two substrings

Asked 2021-Dec-09 at 01:11

From this example string:

...

ANSWER

Answered 2021-Dec-09 at 01:11

use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")

if applied to sample data in your question - output is

Source https://stackoverflow.com/questions/70283253

QUESTION

how to stop letter repeating itself python

Asked 2021-Nov-25 at 18:33

I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it

...

ANSWER

Answered 2021-Nov-25 at 18:33

As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

Source https://stackoverflow.com/questions/70112201

QUESTION

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Asked 2021-Nov-17 at 13:56

I am trying to use plink1.9 to split multiallelic into biallelic. The input is that

...

ANSWER

Answered 2021-Nov-17 at 09:45

I used bcftools to complete the task.

https://github.com/samtools/bcftools/issues/1193

Source https://stackoverflow.com/questions/70001737

QUESTION

Delete specific letter in a FASTA sequence

Asked 2021-Oct-12 at 21:00

I have a FASTA file that has about 300000 sequences but some of the sequences are like these

...

ANSWER

Answered 2021-Oct-12 at 20:28

You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

For example:

Source https://stackoverflow.com/questions/69545912

QUESTION

How to get the words within the first single quote in r using regex?

Asked 2021-Oct-04 at 22:27

For example, I have two strings:

...

ANSWER

Answered 2021-Oct-04 at 22:27

For your example your pattern would be:

Source https://stackoverflow.com/questions/69442717

QUESTION

Does Apache Spark 3 support GPU usage for Spark RDDs?

Asked 2021-Sep-23 at 05:53

I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.

I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.

On querying in Hail forum, I got the response that

That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.

So, does Spark3 not support GPU usage for RDD interfaces?

...

ANSWER

Answered 2021-Sep-23 at 05:53

As of now, spark-rapids doesn't support GPU usage for RDD interfaces.

Source: Link

Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.

Here, an answer from spark-rapids team

Source: Link

We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.

Source https://stackoverflow.com/questions/69273205

QUESTION

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Asked 2021-Sep-07 at 13:09

I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:

...

ANSWER

Answered 2021-Sep-07 at 11:10

a tidyverse solution

Source https://stackoverflow.com/questions/69086946

QUESTION

Usage of compression IO functions in apache arrow

Asked 2021-Jun-02 at 18:58

I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.

...

ANSWER

Answered 2021-Jun-02 at 18:58

Here is an example program that inflates a compressed zlib file and reads it as CSV.

Source https://stackoverflow.com/questions/67799265

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

Vulnerabilities

No vulnerabilities reported

Install celseq2

Running celseq2 pipeline is as easy as 1-2-3. Below is the visualization of the experiment design as same as the sample sheet used in last generation of the pipeline (CEL-Seq-pipeline) as example. The user had two biological samples which could come from two different experiments, two time-points, two types of tissues, or even two labs. They were denoted as squares and circles, respectively. Each sample had 9 cells. In principle, what the user would expect as final output was one UMI count matrix for each sample, which meant two UMI matrices in total in this example. During the CEL-Seq2 experiment, all cells were placed in one 96-well cell plate. They were labeled with same sequencing barcodes (shown as orange plate) but each cell was labeled with its own CEL-Seq2 cell barcode, so that all of them could be sequenced together without losing identities. In details, the nine cells from Experiment-1 were labeled with CEL-Seq2 cell barcodes indexed from 1 to 9, respectively, while the other nine cells from Experiment-2 were labeled with cell barcodes 10 to 18. Finally the library was distributed in two lanes (purple and dark gray bar) of a sequencer, and got sequenced, which resulted in two sets of CEL-Seq2 data (per lane per sequencing barcode). What would the pipeline of celseq2 do for the user was to generate UMI-count matrix per experiment with the two sets of CEL-Seq2 data as input.

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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