Package ubic.gemma.core.loader.expression.singleCell

Class TenXCellRangerUtils

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils

public class TenXCellRangerUtils
extends Object

Utilities for detecting 10x Cell Ranger data in GEO series and sample metadata.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
TenXCellRangerUtils()

Method Summary

Modifier and Type	Method	Description
static boolean	detect10x(String description)	Detect if a description (i.e.
static String	detect10xChemistry(String description)	We essentially rely on the presence of specific production number of reagent kits in the extraction protocol section.
static boolean	detect10xFiltered(String description)	Detect if a description (i.e.
static boolean	detect10xFromMexFile(Path mexFile)
static boolean	detect10xUnfiltered(String description)	Detect if a description (i.e.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TenXCellRangerUtils

public TenXCellRangerUtils()

Method Details

detect10x

public static boolean detect10x(String description)

Detect if a description (i.e. a GEO data processing section) indicates that the data originates from a 10x Cell Ranger platform.

detect10xFiltered

public static boolean detect10xFiltered(String description)

Detect if a description (i.e. a GEO data processing section) indicates that the data is filtered.

detect10xUnfiltered

public static boolean detect10xUnfiltered(String description)

Detect if a description (i.e. a GEO data processing section) indicates that the data is unfiltered.

detect10xFromMexFile

public static boolean detect10xFromMexFile(Path mexFile)

detect10xChemistry

@Nullable
public static String detect10xChemistry(String description)

We essentially rely on the presence of specific production number of reagent kits in the extraction protocol section.

TODO: this will need more work and tests