The term 'RNA-seq'refers to a collection of assays based on sequencing experiments that
involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto …

The increasing availability of genomic resequencing data sets and high-quality reference
genomes across the tree of life present exciting opportunities for comparative population …

Motivation A recurring challenge in interpreting genomic data is the assessment of results in
the context of existing reference databases. With the increasing number of command line …

The family of Malacoherpesviridae is currently represented by only two viruses infecting
molluscs, Ostreid herpesvirus 1 (OsHV-1) and Haliotid herpesvirus 1 (HaHV-1), both …

Abstract Motivation The Gene Expression Omnibus has become an important source of
biological data for secondary analysis. However, there is no simple, programmatic way to …

Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to
support cell specification during development. Naive mouse embryonic stem cells are …

Barcode-based sequence census assays utilize custom or random oligonucloetide
sequences to label various biological features, such as cell-surface proteins or CRISPR …

Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of
the human gut microbiome and play an important role in the infant gut microbiome. These …

Here we developed KARAJ, a fast and flexible Linux command-line tool to automate the end-
to-end process of querying and downloading a wide range of genomic and transcriptomic …

The genomic data deluge has led to challenges with sharing and integrating genomic data.
While substantial effort has been devoted to making genomics data easier to share, one …