Some help header information will go here

Basic sample statistics

End point:

/misra/stat/sample

Parameters:

exp: The ID(s) of the sample (SRA experiment: SRX, ERP or DRP). Several SRA IDs can be given seperated by comas

Example usage:

Single sample

/misra/stat/sample?exp=SRX9773645 Result: Dictionary in JSON format. Keys-->Values. For example, "reads": "13653151" means 13653151 reads in the analysis after adapter trimming and quality control.

Multiple samples

/misra/stat/sample?exp=SRX9773645,SRX9773646 Result: Nested dictionary in JSON format: sample ID --> Keys-->Values.

Mapping statistics

End point:

/misra/stat/mapping

Parameters:

exp: The ID of the sample (SRA experiment: SRX, ERP or DRP).

Example usage:

/misra/stat/mapping?exp=SRX13110001

Result:

JSON format. Keys-->Values. For example, "reads": "13653151" means 13653151 reads in the analysis after adapter trimming and quality control.

IsoMir Data

End point:

/misra/stat/isomir

Parameters:

exp: The ID(s) of the sample (SRA experiment: SRX, ERP or DRP). Several SRA IDs can be given seperated by comas table: one of the following - miRGeneDBiso: MirGeneDB (genome mode) - libsIsomiRBase: "miRBase (genome mode) - libsIsoMirGeneDB: MirGeneDB (library mode) - libsIsomiRBase: miRBase (library mode) - libsIsoPmiren: pMiren (library mode) dict_format: if set, the output will be nested dictionary, outwise

Example usage:

/misra/stat/isomir?exp=SRX9773645:SRX9773646

Result: Dictionary in JSON format. sample_id --> list[dicionary]

/misra/stat/isomir?exp=SRX9773645:SRX9773646&dict_format

Result: Nested dictionary in JSON format: sample_id --> microRNA name --> dictionary

Genome Mapping Statistics

End point:

/misra/stat/genome

Parameters:

exp: The ID(s) of the sample (SRA experiment: SRX, ERP or DRP). Several SRA IDs can be given separated by comas

Result:

Retrieve microRNA Expression Matrix

Obtain a expression matrix in Columns=Samples / Rows=microRNAs or json format (nested dictionary) sample -> miRNA -> expression value

End point:

/misra/stat/matrix

Mandatory Parameters:

One of the two parameters needs to be given:

exp: The SRA experiment IDs given as ',' separated string. For example: /misra/stat/matrix?exp=SRX15239899,SRX1641378

taxon: The taxon ID of the species. All samples of this species will be processed. For example: /misra/stat/matrix?taxon=6945

Optional Parameters:

table: The expression table (Default: libsMirGeneDB). Possible values:

• miRGeneDB: MirGeneDB (genome mode)
• miRBase: "miRBase (genome mode)
• libsMirGeneDB: MirGeneDB (library mode)
• libsmiRBase: miRBase (library mode)
• libsPmiren: pMiren (library mode)

format: Can be 'tsv' or 'csv'. If format is given, a file will be returned in csv or tsv format.

file: The file name. Only applies if format is given.

type: The expression value used in the matrix. Can be:

• RCadj - the adjusted Read Count (default)
• RPMadjLib: the adjusted Read Counts normalized by the number of reads mapped to all microRNAs
• RPMadjTotal: the adjusted Read Counts normalized by the total number of reads in the analysis

Retrieve microRNA Expression Data

Obtain the samples where a given microRNA shows highest expression, either by raw read count or normalized RPM counts

End point:

/misra/stat/mirna

Mandatory Parameters:

mirna: The name of the MATURE microRNA as it appears in MirGeneDB, miRBase or PMiren.

Optional Parameters:

table: The expression table (Default: libsMirGeneDB). Possible values:

• miRGeneDB: MirGeneDB (genome mode)
• miRBase: "miRBase (genome mode)
• libsMirGeneDB: MirGeneDB (library mode)
• libsmiRBase: miRBase (library mode)
• libsPmiren: pMiren (library mode)

file: file name. Returns the result as file. Default: return json data to browser

order_by: Either 'RC','RCadj','RPMadjLib' or 'RPMadjTotal'. Default: order_by=RPMadjLib

limit: The number of samples. Default: limit=20, Maximal allowed: 1000

format: Possible values csv,tsv or json. Default: format=json

Example usage:

/misra/stat/mirna?mirna=Hsa-Mir-1-P1_3p

Result:

Either a file or data in JSON

Retrieve microRNA statistics (total and average counts)

Obtain the total number of counts and the average number of counts of a given microRNA over all samples in the database

End point:

/misra/stat/mirnastat

Mandatory Parameters:

mirna: The name of the MATURE microRNA as it appears in MirGeneDB, miRBase or PMiren. A coma separated string can be provided.

Optional Parameters:

table: The expression table (Default: libsMirGeneDB). Possible values:

• miRGeneDB: MirGeneDB (genome mode)
• miRBase: "miRBase (genome mode)
• libsMirGeneDB: MirGeneDB (library mode)
• libsmiRBase: miRBase (library mode)
• libsPmiren: pMiren (library mode)

Example usage:

/misra/stat/mirnastat?mirna=Isc-Mir-375_3p,Isc-Mir-10-P2_5p

Result:

Data in JSON