We fit subsets of data provided at https://data.caltech.edu/records/2017 using a Markov modeling of mRNA transcription, splicing, degradation, and sequencing. The following files are provided: raw_results.tar.gz: raw result files output by fitting each dataset. These files should be analyzed by using the import_datasets functionality. processe...

We processed a set of 10X datasets using kallisto|bustools. The archive contains filtered loom files. The scripts used to generate these files are provided at https://github.com/pachterlab/GP_2021_3/tree/master/processing_scripts.

This package includes the MATLAB app GUI, source code, and search algorithm for the preprint "Stochastic simulation platform for visualization and estimation of transcriptional kinetics." The GUI simulates and visualizes RNA transcription; the source code allows implementation of more complex reaction schema; the search algorithm performs parame...

This dataset contains ten 10X scRNA-seq datasets (two v2 from Desai et al., DOI: 10.1126/science.abc6506, eight v3 generated by 10X Genomics) that have been processed using pipelines for spliced and unspliced molecule quantification. We used velocyto, kallisto|bustools (kb), and salmon/alevin-fry to process the raw FASTQ files, and output loompy...

Metadata for 10x Genomics (v3) 10k PBMC data. Zip file includes an initial K-Means clustering on the data (K=4) and a list of literature markers for PBMCs. 

Output from kb ref for the mm10-2020-A mouse genome with intron and exon annotations. For use with Monod and meK-Means CME modeling of U and S counts.

Output from kb ref for the GRCh38-2020-A genome with intron and exon annotations. For use with Monod and meK-Means CME modeling of U and S counts.

Dataset for "Protein velocity and acceleration from single-cell multiomics experiments." Source data from 10X Genomics at https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_1k_protein_v3 and https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_protein_v3.

Protein count data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2685243, file GSM2685243_protein_2_PBMCs_matrix.txt.gz, and processed into csv format. Aligned bam file was acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2685238, file mRNA_2_PBMCs_possorted_genome_bam.bam. velocyto processing: ve...

Protein data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3596101, file GSM3596101_CTCL-ADT-count.csv.gz. velocyto processing: velocyto run (bam directory)/(BAM file).bam (transcriptome directory)/genes/genes.gtf