SEQC is a python package that processes single-cell sequencing data in the cloud and analyzes it interactively on your local machine.

Summary from the GEO: "Linker histone H1 proteins bind to nucleosomes and cause chromatin compaction, although little is known about their biological functions. Histone H1 (HIST1H1B-E) mutations are highly recurrent in B-cell lymphomas and are present in solid tumors, but their cancer relevance and mechanism are unknown. Here we report that lymphoma-associated H1 alleles are genetic driver mutations...

BioProject description: "Genome sequencing of Listeria seeligeri LS46 and LS59". The whole genome sequencing of these listeriaphage enabled researchers to discover that AcrVIA1, an anti-CRISPR protein, interacts with the guide-exposed face of Cas13a, a (crRNA)-guided nuclease, preventing access to the target RNA and the conformational changes required for nuclease activation. A single dose of AcrVIA1...

R scripts used to for data analysis and figure support for the manuscript: Wipperman, M.F., Bhattarai, S.K., Vorkas, C.K. et al. Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. Nat Commun 12, 1141 (2021). Data is available for download from Dropbox and the scripts listed are accessible from GitHub.

Description from EGA: "DNA methylation sequencing profiles of 1538 breast tumors and 244 normal breast tissues. Libraries were prepared using a custom Reduced Representation Bisulfite Sequencing pipeline. Sequencing was performed on the Illumina HiSeq 2500 (v4 chemistry), with single-end reads of 125 bp length. Multiplexing was conducted at the level of 8 samples per lane. FASTQ files are provided...

Description from EGA: "Affymetrix 6.0 cel files" Part of the METABRIC data access committee study, accession number EGAC0000100048

This dataset contains summary data visualizations and clinical data from targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). This data is available under the Creative Commons BY-NC-ND 4.0 license. For commercial use, please contact datarequests@mskcc.org....

This dataset contains summary data visualizations and clinical data from target sequencing analysis of 2509 primary breast tumors from 2,509 patients. The study was conducted to identify putative cancer genes, revealing novel subgroups with distinct clinical outcomes. The results were validated by long-term clinical follow-up. The clinical data includes mutated genes, 3-gene classifier subtypes, and...