mojaveazure / utilities

A repository full of bioinformatics-related utilities

Hello World

I am Paul Hoffman, a senior bioinformatician with the Satija and Lappalainen Labs at the New York Genome Center. My work revolves around building software and for bioinformatic analyses, including an R package for analyzing single-cell data, along with several extension packages, and a pipeline for processing RNA-seq data. I work primarily in R and Python, but am always learning.

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Recent Activity

• Closed TileDB-Inc/tiledbsc#92
• Merged single-cell-data/TileDB-SOMA#990
• Opened single-cell-data/TileDB-SOMA#990
• Closed TileDB-Inc/TileDB-R#518
• Merged TileDB-Inc/TileDB-R#519
• Opened TileDB-Inc/TileDB-R#519
• Opened TileDB-Inc/TileDB-R#518
• Opened bnprks/BPCells#3
• Closed satijalab/seurat#6539
• Closed satijalab/seurat#6692

utilities's Issues

BLAST_to_BED.py does not picked mapped hit

In some cases, BLAST against the draft reference may return a hit to both a mapped and unmapped position. We obviously prefer information on the mapped position. A example of a gene where this occurs is alpha amylase type B locus, chrUn 184040827 184041686 gi|532003875|gb|KC963100.1| Hordeum vulgare subsp. vulgare cultivar Morex alpha-amylase type B (Aamy) gene, partial cds chrUn 184040686 184042502.

BLAST_to_BED should run with a database, not subject sequence

Like the title says...