hms-dbmi hidive-dmp-requirements issues

hms-dbmi / hidive-dmp-requirements

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Current challenges with data computation for the purpose of visualization in Gosling and other applications

#32 sehilyi opened 8 months ago
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Users should be able to query data subsets based regions of interest (e.g., by genomic coordinates)

#31 astridvandenbrandt opened 8 months ago
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The platform should hint at file format inconsistencies/issues and help the user correct them

#30 astridvandenbrandt opened 8 months ago
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The user should be able to access basic summary statistics of the (linked) data files (e.g., # sample IDs, dimensions) for quick validation

#29 astridvandenbrandt opened 8 months ago
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Users need to discover data across the CFDE

#28 keller-mark opened 8 months ago
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File metadata should indicate whether multiple files are comparable to each other

#27 keller-mark opened 8 months ago
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Users should be able to use the platform through API (e.g., Python, TS, etc)

#26 sehilyi opened 8 months ago
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Users should be able to use the platform through GUI

#25 sehilyi opened 8 months ago
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Expression matrices must be annotated with the type of normalization that has been applied

#24 keller-mark opened 8 months ago
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Files need to be annotated with the Vitessce data types that they contain and internal relative paths to those contents

#23 keller-mark opened 8 months ago
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Users should be able to create their account for the platform

#22 sehilyi opened 8 months ago
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The platform should provide an option to use freely

#21 sehilyi opened 8 months ago
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Users should be able to use their own data instance as the main instance behind the platform (e.g., Amazon EC2)

#20 sehilyi opened 8 months ago
1
Users should be able to share data by inviting other users to the 'project' or a 'group' (e.g., adding accounts)

#19 sehilyi opened 8 months ago
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The platform should be able to convert files to similar and visualization-supported formats when users request (e.g., SAMs to BAMs)

#18 sehilyi opened 8 months ago
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Users should be able to manage the version of data and metadata in the platform

#17 sehilyi opened 8 months ago
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The platform should process metadata ('knowledge') from a submitted file, e.g., whether there is mutation(s) near a gene of interest or inferred VCF from BAM

#16 sehilyi opened 9 months ago
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Users should make their data accessible only with proper authentication (e.g., private code or account)

#15 sehilyi opened 9 months ago
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Users should be able to determine the duration of file accessibility (e.g., expires in 10 days)

#14 sehilyi opened 9 months ago
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Users should be able to easily validate the submitted data using the platform with a visualization

#13 sehilyi opened 9 months ago
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Users should be able to retrieve the metadata of file(s) (e.g., linked disease of files)

#12 sehilyi opened 9 months ago
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Users should be able to retrieve HTTP endpoints of the list of files based on the metadata filtering (e.g., set of files having the same Sample ID)

#11 sehilyi opened 9 months ago
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Users should be able to link to external datasets (e.g., files stored at Amazon S3)

#10 sehilyi opened 9 months ago
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Users should be able to upload files using the platform from the local machine

#9 sehilyi opened 9 months ago
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Users should be able to add a list of quantitative, qualitative, or hierarchical values as metadata to a single file (e.g., quality measures of samples in a multivec file)

#8 sehilyi opened 9 months ago
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Users should be able to add quantitative and qualitative metadata to a single file (e.g., an experiment condition, quality score, citation)

#7 sehilyi opened 9 months ago
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Users should be able to add metadata to a set of files (e.g., sample ID, disease, and note that correspond to a set of files)

#6 sehilyi opened 9 months ago
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The platform should store basic metadata about genomics files (e.g., data types, file types, file size, assembly)

#5 sehilyi opened 9 months ago
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The platform should sort files (e.g., chromosomes) when needed to properly show data in visualization

#4 sehilyi opened 9 months ago
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The platform should generate missing index files when needed for visualizations (e.g., BAI for BAM, Tabix for VCF and GFF)

#3 sehilyi opened 9 months ago
1
The platform should process data to generate HiGlass-server-compatible data when users request (e.g., standard BED to HiGlass' BEDDB)

#2 sehilyi opened 9 months ago
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Users should be able to easily add HiGlass data (e.g., multivec) to a HiGlass server

#1 sehilyi opened 9 months ago
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