ARCHS4 Workshop
ARCHS4: Massive Mining of Publicly Available RNA-seq Data from Human and Mouse
All RNA-seq and ChIP-seq sample and signature search (ARCHS4) is a resource that provides access to gene and transcript counts uniformly processed from all human and mouse RNA-seq experiments from the Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA).
The ARCHS4 website provides the uniformly processed data for download and programmatic access in H5 format, and as a 3-dimensional interactive viewer and search engine.
Users can search and browse the data by metadata enhanced annotations, and can submit their own gene sets for search. Subsets of selected samples can be downloaded as a tab delimited text file that is ready for loading into the R programming environment. To generate the ARCHS4 resource, the kallisto aligner is applied in an efficient parallelized cloud infrastructure. Human and mouse samples are aligned against GRCh38 and GRCm39 with Ensembl annotation (Ensembl 107).
ARCHS4 Workshop
The workshop is designed to provide overall information on ARCHS4 for users as well as the general concept of gene expression and alignment for beginners. It will be led by Alexander Lachmann, Ph.D., who is an assistant professor at Ma’ayan laboratory and developed ARCHS4.
The schedule for the workshop is as follows.
| Time (EST) | Object |
|---|---|
| 2:00 PM | Welcome & Introduction |
| 2:05 PM | Basics on Gene Expression and Alignment |
| 2:30 PM | Kallisto, one of the leading algorithms on gene alignment |
| 3:00 PM | ARCHS4 : Introduction |
| 3:05 PM | ARCHS4 : Programmatic approach |
| 3:20 PM | ARCHS4 : Use cases |
| 3:30 PM | ARCHS4 : Live Demo |
| 3:50 PM | Q&A Session |
More information is available at: ARCHS4 Website | Publication | Ma’ayan Laboratory