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Fire Browse Beta API Retrieve all data by genes Gistic2 results.

This service provides access to the Gistic2 all_data_by_genes.txt output data. This data is a gene-level table of copy number values for all samples. The returned copy number values are in units (copy number - 2) so that no amplification or deleti...

Fire Browse Beta API Retrieve Gistic2 significantly amplified genes results.

This service provides access to the Gistic2 amp_genes.conf_99.txt output data. At least 1 gene or cohort must be supplied.

Fire Browse Beta API Retrieve Gistic2 significantly deleted genes results.

This service provides access to the Gistic2 del_genes.conf_99.txt output data. At least 1 gene or cohort must be supplied.

Fire Browse Beta API Retrieve focal data by genes Gistic2 results.

This service provides access to the Gistic2 focal_data_by_genes.txt output data. This output is similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. This data is a gene-level ...

Fire Browse Beta API Retrieve all thresholded by genes Gistic2 results.

This service provides access to the Gistic2 all_thresholded_by_genes.txt output data. A gene-level table of discrete amplification and deletion indicators for all samples. A table value of 0 means no amplification or deletion above the threshold. ...

Fire Browse Beta API Retrieve aggregated analysis features table.

This service returns part or all of the so-called feature table; which aggregates the most important findings across ALL pipelines in the GDAC Firehose analysis workflow into a single table for simple access. One feature table is created per dise...

Fire Browse Beta API Returns RNASeq expression quartiles, e.g. suitable for drawing a boxplot.

For a given gene compute quartiles and extrema, suitable e.g. for drawing a boxplot (Tukey 1977). Results may be filtered by cohort, sample type, patient barcode or characterization protocol, and are returned sorted by cohort. Note that samples...

Fire Browse Beta API Retrieve MutSig final analysis MAF.

This service returns columns from the MAF generated by MutSig. Results may be filtered by gene, cohort, tool, or barcode, but at least one gene OR barcode OR cohort must be given. By default a subset consisting of the most commonly used columns w...

Fire Browse Beta API Retrieve Significantly Mutated Genes (SMG).

This service provides a list of significantly mutated genes, as scored by MutSig. It may be filtered by cohort, rank, gene, tool and/or Q-value threshold, but at least one cohort or gene must be supplied.

Fire Browse Beta API Retrieve links to summary reports from Firehose analysis runs.

This service returns URLs to the analysis result reports for runs of the Broad Institute GDAC Firehose analysis pipeline. At least one year of run reports are maintained in the database, but the reports from the latest run will be returned by defa...

Fire Browse Beta API Retrieve standard data archives.

This service returns the archive URLs for our Firehose standard data runs, providing a RESTful interface similar in spirit to the command line firehose_get tool. The archives can be filtered based on date, cohort, data type, platform, center, data...

Fire Browse Beta API Obtain identities of TCGA consortium member centers.

By default this function returns a table of all consortium members in TCGA, aka centers; it provides both the HTTP domain and full organizational name of each center. A subset of this table may be obtained by explicitly specifying one or more dom...

Fire Browse Beta API Retrieve names of CDEs normalized by Firehose and selected for analyses.

This service returns the names of patient-level clinical data elements (CDEs) that have been normalized by Firehose for use in analyses, unioned across all disease cohorts. For more information on how these CDEs are processed, see our pipeline doc...

Fire Browse Beta API Retrieve names of all TCGA clinical data elements (CDEs).

Retrieve names of all patient-level clinical data elements (CDES) available in TCGA, unioned across all disease cohorts. A CDE will be listed here only when it has a value other than NA for at least 1 patient case in any disease cohort. For more i...

Fire Browse Beta API Translate TCGA cohort abbreviations to full disease names.

By default this function returns a table containing all TCGA cohort abbreviations and their corresponding disease names. A subset of that table may be obtained by explicitly specifying one or more cohort abbreviations.

Fire Browse Beta API Retrieve sample counts.

Returns the aliquot counts for each disease cohort, per sample type and data type. The sample type designation of "Tumor" may be used to aggregate the count of all tumor aliquots into a single number per disease and data type. See the SampleTypes...

Fire Browse Beta API Retrieve datestamps of all GDAC Firehose standard data and analyses runs that have been ingested into FireBrowse.

Retrieve datestamps of all gdac firehose standard data and analyses runs that have been ingested into firebrowse..

Fire Browse Beta API Simple way to discern whether API server is up and running

Returns a message to indicate that API (server) is up and running, or times out if not.

Fire Browse Beta API Retrieve names of all columns in the mutation annotation files (MAFs) served by FireBrowse.

Retrieve the names of all columns in the mutation annotation files (MAFs) hosted by FireBrowse. For more information on the mutation data, and how it is processed by Firehose, please consult the pipeline documentation.

Fire Browse Beta API Retrieve list of all TCGA patients.

This service returns a list of all TCGA patient barcodes in FireBrowse, optionally filtered by disease cohort. The barcodes are obtained directy from the clinical data.

Fire Browse Beta API Translate TCGA platform codes to full platform names.

By default this function returns a table of all of the technology platforms used to sequence or characterize samples in TCGA--both their short platform codes and full names. A subset of this table may be obtained by explicitly specifying one or m...

Fire Browse Beta API Given a TCGA barcode, return its short letter sample type code.

Given a tcga barcode, return its short letter sample type code..

Fire Browse Beta API Translate from numeric to symbolic TCGA sample codes.

Convert a TCGA numeric sample type code (e.g. 01, 02) to its corresponding symbolic (short letter) code (e.g. TP, TR).

Fire Browse Beta API Return all TCGA sample type codes, both numeric and symbolic.

Return all tcga sample type codes, both numeric and symbolic..

Fire Browse Beta API Translate from symbolic to numeric TCGA sample codes.

Convert a TCGA sample type code in symbolic form (or 'short letter code' like TP, TR) to its corresponding numeric form (e.g. 01, 02).

Fire Browse Beta API Obtain identities of tissue source sites in TCGA.

By default this function returns a table of all sites which contributed source tissue to TCGA, aka TSS's. A subset of this table may be obtained by explicitly specifying one or more sites.

Fire Browse Beta API Retrieve CDEs normalized by Firehose and selected for analyses.

This service returns patient-level clinical data elements (CDEs) that have been normalized by Firehose for use in analyses. Results may be selected by disease cohort, patient barcode or CDE name, but at least one cohort, barcode or CDE must be pro...

Fire Browse Beta API Retrieve TCGA CDEs verbatim, i.e. not normalized by Firehose.

This service returns patient clinical data from TCGA, verbatim. It differs from the Samples/Clinical_FH method by providing access to all TCGA CDEs in their original form, not merely the subset of CDEs normalized by Firehose for analyses. Results...

Fire Browse Beta API Retrieve miRSeq data.

This service returns sample-level log2 miRSeq expression values. Results may be filtered by miR, cohort, barcode, sample type or Firehose preprocessing tool, but at least one miR must be supplied.

Fire Browse Beta API Retrieve mRNASeq data.

This service returns sample-level log2 mRNASeq expression values. Results may be filtered by gene, cohort, barcode, sample type or characterization protocol, but at least one gene must be supplied.

Fire Browse Retrieve all data by genes Gistic2 results.

This service provides access to the Gistic2 all_data_by_genes.txt output data. This data is a gene-level table of copy number values for all samples. The returned copy number values are in units (copy number - 2) so that no amplification or deleti...

Fire Browse Retrieve Gistic2 significantly amplified genes results.

This service provides access to the Gistic2 amp_genes.conf_99.txt output data. At least 1 gene or cohort must be supplied.

Fire Browse Retrieve Gistic2 significantly deleted genes results.

This service provides access to the Gistic2 del_genes.conf_99.txt output data. At least 1 gene or cohort must be supplied.

Fire Browse Retrieve focal data by genes Gistic2 results.

This service provides access to the Gistic2 focal_data_by_genes.txt output data. This output is similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. This data is a gene-level ...

Fire Browse Retrieve all thresholded by genes Gistic2 results.

This service provides access to the Gistic2 all_thresholded_by_genes.txt output data. A gene-level table of discrete amplification and deletion indicators for all samples. A table value of 0 means no amplification or deletion above the threshold. ...

Fire Browse Retrieve aggregated analysis features table.

This service returns part or all of the so-called feature table; which aggregates the most important findings across ALL pipelines in the GDAC Firehose analysis workflow into a single table for simple access. One feature table is created per dise...

Fire Browse Returns RNASeq expression quartiles, e.g. suitable for drawing a boxplot.

For a given gene compute quartiles and extrema, suitable e.g. for drawing a boxplot (Tukey 1977). Results may be filtered by cohort, sample type, patient barcode or characterization protocol, and are returned sorted by cohort. Note that samples...

Fire Browse Retrieve MutSig final analysis MAF.

This service returns columns from the MAF generated by MutSig. Results may be filtered by gene, cohort, tool, or barcode, but at least one gene OR barcode OR cohort must be given. By default a subset consisting of the most commonly used columns w...

Fire Browse Retrieve Significantly Mutated Genes (SMG).

This service provides a list of significantly mutated genes, as scored by MutSig. It may be filtered by cohort, rank, gene, tool and/or Q-value threshold, but at least one cohort or gene must be supplied.

Fire Browse Retrieve links to summary reports from Firehose analysis runs.

This service returns URLs to the analysis result reports for runs of the Broad Institute GDAC Firehose analysis pipeline. At least one year of run reports are maintained in the database, but the reports from the latest run will be returned by defa...

Fire Browse Retrieve standard data archives.

This service returns the archive URLs for our Firehose standard data runs, providing a RESTful interface similar in spirit to the command line firehose_get tool. The archives can be filtered based on date, cohort, data type, platform, center, data...

Fire Browse Obtain identities of TCGA consortium member centers.

By default this function returns a table of all consortium members in TCGA, aka centers; it provides both the HTTP domain and full organizational name of each center. A subset of this table may be obtained by explicitly specifying one or more dom...

Fire Browse Retrieve names of CDEs normalized by Firehose and selected for analyses.

This service returns the names of patient-level clinical data elements (CDEs) that have been normalized by Firehose for use in analyses, unioned across all disease cohorts. For more information on how these CDEs are processed, see our pipeline doc...

Fire Browse Retrieve names of all TCGA clinical data elements (CDEs).

Retrieve names of all patient-level clinical data elements (CDES) available in TCGA, unioned across all disease cohorts. A CDE will be listed here only when it has a value other than NA for at least 1 patient case in any disease cohort. For more i...

Fire Browse Translate TCGA cohort abbreviations to full disease names.

By default this function returns a table containing all TCGA cohort abbreviations and their corresponding disease names. A subset of that table may be obtained by explicitly specifying one or more cohort abbreviations.

Fire Browse Retrieve sample counts.

Returns the aliquot counts for each disease cohort, per sample type and data type. The sample type designation of "Tumor" may be used to aggregate the count of all tumor aliquots into a single number per disease and data type. See the SampleTypes...

Fire Browse Retrieve datestamps of all GDAC Firehose standard data and analyses runs that have been ingested into FireBrowse.

Retrieve datestamps of all gdac firehose standard data and analyses runs that have been ingested into firebrowse..

Fire Browse Simple way to discern whether API server is up and running

Returns a message to indicate that API (server) is up and running, or times out if not.

Fire Browse Retrieve names of all columns in the mutation annotation files (MAFs) served by FireBrowse.

Retrieve the names of all columns in the mutation annotation files (MAFs) hosted by FireBrowse. For more information on the mutation data, and how it is processed by Firehose, please consult the pipeline documentation.

Fire Browse Retrieve list of all TCGA patients.

This service returns a list of all TCGA patient barcodes in FireBrowse, optionally filtered by disease cohort. The barcodes are obtained directy from the clinical data.

Fire Browse Translate TCGA platform codes to full platform names.

By default this function returns a table of all of the technology platforms used to sequence or characterize samples in TCGA--both their short platform codes and full names. A subset of this table may be obtained by explicitly specifying one or m...

Fire Browse Given a TCGA barcode, return its short letter sample type code.

Given a tcga barcode, return its short letter sample type code..

Fire Browse Translate from numeric to symbolic TCGA sample codes.

Convert a TCGA numeric sample type code (e.g. 01, 02) to its corresponding symbolic (short letter) code (e.g. TP, TR).

Fire Browse Return all TCGA sample type codes, both numeric and symbolic.

Return all tcga sample type codes, both numeric and symbolic..

Fire Browse Translate from symbolic to numeric TCGA sample codes.

Convert a TCGA sample type code in symbolic form (or 'short letter code' like TP, TR) to its corresponding numeric form (e.g. 01, 02).

Fire Browse Obtain identities of tissue source sites in TCGA.

By default this function returns a table of all sites which contributed source tissue to TCGA, aka TSS's. A subset of this table may be obtained by explicitly specifying one or more sites.

Fire Browse Retrieve CDEs normalized by Firehose and selected for analyses.

This service returns patient-level clinical data elements (CDEs) that have been normalized by Firehose for use in analyses. Results may be selected by disease cohort, patient barcode or CDE name, but at least one cohort, barcode or CDE must be pro...

Fire Browse Retrieve TCGA CDEs verbatim, i.e. not normalized by Firehose.

This service returns patient clinical data from TCGA, verbatim. It differs from the Samples/Clinical_FH method by providing access to all TCGA CDEs in their original form, not merely the subset of CDEs normalized by Firehose for analyses. Results...

Fire Browse Retrieve miRSeq data.

This service returns sample-level log2 miRSeq expression values. Results may be filtered by miR, cohort, barcode, sample type or Firehose preprocessing tool, but at least one miR must be supplied.

Fire Browse Retrieve mRNASeq data.

This service returns sample-level log2 mRNASeq expression values. Results may be filtered by gene, cohort, barcode, sample type or characterization protocol, but at least one gene must be supplied.

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