JarCasting
JarCasting JarCasting

TenxKit


License

License

MIT
GroupId

GroupId

com.github.biopet
ArtifactId

ArtifactId

tenxkit_2.11
Last Version

Last Version

0.1
Release Date

Release Date
Type

Type

jar
Description

Description

TenxKit
TenxKit
Project URL

Project URL

https://github.com/biopet/10xkit
Project Organization

Project Organization

Biopet
Source Code Management

Source Code Management

https://github.com/biopet/10xkit

Download tenxkit_2.11

Filename Size
tenxkit_2.11-0.1.pom
tenxkit_2.11-0.1.jar 987 KB
tenxkit_2.11-0.1-sources.jar 75 KB
tenxkit_2.11-0.1-javadoc.jar 635 KB
Browse

How to add to project

<!-- https://jarcasting.com/artifacts/com.github.biopet/tenxkit_2.11/ -->
<dependency>
    <groupId>com.github.biopet</groupId>
    <artifactId>tenxkit_2.11</artifactId>
    <version>0.1</version>
</dependency>
// https://jarcasting.com/artifacts/com.github.biopet/tenxkit_2.11/
implementation 'com.github.biopet:tenxkit_2.11:0.1'
// https://jarcasting.com/artifacts/com.github.biopet/tenxkit_2.11/
implementation ("com.github.biopet:tenxkit_2.11:0.1")
'com.github.biopet:tenxkit_2.11:jar:0.1'
<dependency org="com.github.biopet" name="tenxkit_2.11" rev="0.1">
  <artifact name="tenxkit_2.11" type="jar" />
</dependency>
@Grapes(
@Grab(group='com.github.biopet', module='tenxkit_2.11', version='0.1')
)
libraryDependencies += "com.github.biopet" % "tenxkit_2.11" % "0.1"
[com.github.biopet/tenxkit_2.11 "0.1"]

Dependencies

compile (5)

Group / Artifact Type Version
org.scala-lang : scala-library jar 2.11.12
com.github.biopet : spark-utils_2.11 jar 0.4
com.github.biopet : tool-utils_2.11 jar 0.4
colt : colt jar 1.2.0
org.bdgenomics.adam : adam-core-spark2_2.11 jar 0.24.0

provided (3)

Group / Artifact Type Version
org.apache.spark : spark-core_2.11 jar 2.3.0
org.apache.spark : spark-sql_2.11 jar 2.3.0
org.apache.spark : spark-mllib_2.11 jar 2.3.0

test (1)

Group / Artifact Type Version
com.github.biopet : tool-test-utils_2.11 jar 0.2.2

Project Modules

There are no modules declared in this project.

TenxKit

Tools - CellReads

This tool will generate a histogram of reads per cell barcode. This can be used to validate output from cellranger or to set a alternative cutoff.

Tools - CellVariantcaller

This tool will call variants based on 10x data. Usually the output of cellranger is used. Each cell will be treated a separated sample.

Tools - CalulateDistance

This tool will calculate for each cell combination a sum of distances. The distances are the relative distance to the middle line for each allele divided by the total coverage on that position.

Tools - GroupDistance

This tool we try to group distances together. The result should be a clusters of 1 single sample.

This tool will execute multiple iterations to find the groups.

Tools - MergeBams

This tool can merge separated 10x experiments into a single bam file. This is used to simulate a mixed run. This is used as a control for the GroupDistance tool.

Tools - EvalSubGroups

This tool will compare all given groups. The histogram for a Correct match should be a steep histogram starting at 0. When multiple peaks are seen this might be a mixture of samples.

Tools - ExtractGroupVariants

This tool will merge variants from the same group. This will be a representation of the real samples. This can also be used to validate if there is a true set known.

Tools - ExtractCellFastqs

This tools will extract fastq files for a given list of cell barcodes. All reads that are marked as duplicate or secondary will be skipped by default.

Documentation

For documentation and manuals visit our github.io page.

About

TenxKit is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contact

For any question related to TenxKit, please use the github issue tracker or contact the SASC team directly at: [email protected].

com.github.biopet

Biopet

Versions

Version
0.1