This dataset contains kallisto quantifications of GSE37704 performed with 100 bootstraps.
", "doi": "10.22002/3scww-j5644", "publisher": "CaltechDATA", "publication_date": "2026-02-16" }, { "id": "data:j57wp-0pp06", "collection": "data", "collection_id": "j57wp-0pp06", "cite_using_url": "https://data.caltech.edu/records/j57wp-0pp06", "type": "dataset", "title": "Transcriptomic responses to endurance exercise training in rats", "author": [ { "family_name": "Oakes", "given_name": "Conrad", "orcid": "0000-0002-8936-055X" }, { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231" } ], "abstract": "All data sets used for data analysis, including post-processing results
", "doi": "10.22002/j57wp-0pp06", "publisher": "CaltechDATA", "publication_date": "2025-07-01" }, { "id": "data:krqmp-5hy81", "collection": "data", "collection_id": "krqmp-5hy81", "cite_using_url": "https://data.caltech.edu/records/krqmp-5hy81", "type": "dataset", "title": "Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression", "author": [ { "family_name": "Luebbert", "given_name": "Laura", "orcid": "0000-0003-1379-2927" }, { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231" } ], "abstract": "Single-cell RNA sequencing count matrices and other data generated in the manuscript \"Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression\". The code used to generate these files can be found here: https://github.com/pachterlab/LSCHWCP_2023
If you use this data, please cite the manuscript:
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristjan Eldjarn Hjorleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter (2023). Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. bioRxiv 2023.12.11.571168; doi: https://doi.org/10.1101/2023.12.11.571168
View the manuscript here: https://www.biorxiv.org/content/10.1101/2023.12.11.571168
", "doi": "10.22002/krqmp-5hy81", "publisher": "CaltechDATA", "publication_date": "2024-05-04" }, { "id": "data:k7xqw-88d74", "collection": "data", "collection_id": "k7xqw-88d74", "cite_using_url": "https://data.caltech.edu/records/k7xqw-88d74", "type": "dataset", "title": "Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression (continued)", "author": [ { "family_name": "Luebbert", "given_name": "Laura", "orcid": "0000-0003-1379-2927" }, { "family_name": "Pachter", "given_name": "Lior", "orcid": "0000-0002-9164-6231" } ], "abstract": "Single-cell RNA sequencing count matrices and other data generated in the manuscript \"Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression\". The code used to generate these files can be found here: https://github.com/pachterlab/LSCHWCP_2023
If you use this data, please cite the manuscript:
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristjan Eldjarn Hjorleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter (2023). Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. bioRxiv 2023.12.11.571168; doi: https://doi.org/10.1101/2023.12.11.571168
View the manuscript here: https://www.biorxiv.org/content/10.1101/2023.12.11.571168
", "doi": "10.22002/k7xqw-88d74", "publisher": "CaltechDATA", "publication_date": "2023-12-12" }, { "id": "data:4t75c-36298", "collection": "data", "collection_id": "4t75c-36298", "cite_using_url": "https://data.caltech.edu/records/4t75c-36298", "type": "dataset", "title": "10X protein and mRNA counts", "author": [ { "family_name": "Gorin", "given_name": "Gennady", "orcid": "0000-0001-6097-2029" }, { "family_name": "Svensson", "given_name": "Valentine", "orcid": "0000-0002-9217-2330" }, { "family_name": "Pachter", "given_name": "Lior", "orcid": "0000-0002-9164-6231" } ], "abstract": "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.", "doi": "10.22002/D1.1339", "publisher": "CaltechDATA", "publication_date": "2020-01-22" }, { "id": "data:sr3vk-qmf10", "collection": "data", "collection_id": "sr3vk-qmf10", "cite_using_url": "https://data.caltech.edu/records/sr3vk-qmf10", "type": "dataset", "title": "CITE-seq protein and mRNA counts", "author": [ { "family_name": "Gorin", "given_name": "Gennady", "orcid": "0000-0001-6097-2029" }, { "family_name": "Svensson", "given_name": "Valentine", "orcid": "0000-0002-9217-2330" }, { "family_name": "Pachter", "given_name": "Lior", "orcid": "0000-0002-9164-6231" } ], "abstract": "Protein counts were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866.\n\nLOOM was generated from FASTQ.\ncellranger processing:\n\ncellranger count --id=(desired bam directory) --transcriptome=(transcriptome directory) --fastqs=(fastq directory) --localcores=40 --localmem=100 --chemistry=SC3Pv2\n\nvelocyto processing:\n\nvelocyto run10x --samtools-threads 60 --samtools-memory 5000 (desired bam directory) (transcriptome directory)/genes/genes.gtf", "doi": "10.22002/D1.1340", "publisher": "CaltechDATA", "publication_date": "2020-01-22" }, { "id": "data:wpc5r-pn556", "collection": "data", "collection_id": "wpc5r-pn556", "cite_using_url": "https://data.caltech.edu/records/wpc5r-pn556", "type": "dataset", "title": "REAP-seq protein and mRNA counts", "author": [ { "family_name": "Gorin", "given_name": "Gennady", "orcid": "0000-0001-6097-2029" }, { "family_name": "Svensson", "given_name": "Valentine", "orcid": "0000-0002-9217-2330" }, { "family_name": "Pachter", "given_name": "Lior", "orcid": "0000-0002-9164-6231" } ], "abstract": "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.\n\nAligned 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.\n\nvelocyto processing:\n\nvelocyto run (bam directory)/mRNA_2_PBMCs_possorted_genome_bam.bam(transcriptome directory)/genes/genes.gtf", "doi": "10.22002/D1.1341", "publisher": "CaltechDATA", "publication_date": "2020-01-22" }, { "id": "data:ab17s-18z31", "collection": "data", "collection_id": "ab17s-18z31", "cite_using_url": "https://data.caltech.edu/records/ab17s-18z31", "type": "dataset", "title": "ECCITE-seq protein and mRNA counts", "author": [ { "family_name": "Gorin", "given_name": "Gennady", "orcid": "0000-0001-6097-2029" }, { "family_name": "Svensson", "given_name": "Valentine", "orcid": "0000-0002-9217-2330" }, { "family_name": "Pachter", "given_name": "Lior", "orcid": "0000-0002-9164-6231" } ], "abstract": "Protein data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3596101, file GSM3596101_CTCL-ADT-count.csv.gz.\n\nvelocyto processing:\n\nvelocyto run (bam directory)/(BAM file).bam (transcriptome directory)/genes/genes.gtf", "doi": "10.22002/D1.1342", "publisher": "CaltechDATA", "publication_date": "2020-01-22" } ]