Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. Homepage: URL: Keyword:bioĭescription: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Homepage: Keyword:physĭescription: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Jack Deslippe, Georgy Samsonidze, David A. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.

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