Python Codebase for SeqC (SEquence Quality Control)

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 10388

Author(s): Carr, Ambrose James*, Choi, Kristy, Pe'er, Dana* * MSK affiliated

Description: SEQC is a python package that processes single-cell sequencing data in the cloud and analyzes it interactively on your local machine.
Timeframe: 2015 - Present

Subject(s)

Access via GitHub
Code and installation instructions for application
Access Restrictions: Free to All
Access Instructions: Code files are available for viewing, download, or clone through GitHub, including list of dependencies and installation instructions in the README.md
Associated Publications: Azizi E, Carr A, Plitas G, et al. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell. 2018; 174(5):1293-1308.e36.
Data Type: Genomic
Software Used: hdf5
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.

STAR Aligner
Spliced Transcripts Alignment to a Reference
Dataset Format(s): Python

Do you have or know of a dataset that should be added to the catalog? Let us know!