Tools

Resources and tools developed by the lab

DIEM (Debris Identification using Expectation Maximization)

More information: Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM. Sci Rep. 2020 07 03; 10(1):11019. Alvarez M, Rahmani E, Jew B, Garske KM, Miao Z, Benhammou JN, Ye CJ, Pisegna JR, Pietiläinen KH, Halperin E, Pajukanta P. PMID: 32620816; PMCID: PMC7335186.
Access DIEM Code on GitHub

Bisque

More information: Accurate estimation of cell composition in bulk expression through robust integration of single-cell information. Nat Commun. 2020 Apr 24; 11(1):1971. Jew B, Alvarez M, Rahmani E, Miao Z, Ko A, Garske KM, Sul JH, Pietiläinen KH, Pajukanta P, Halperin E. PMID: 32332754; PMCID: PMC7181686.
Access Bisque Code on GitHub

ASElux

More information: ASElux: an ultra-fast and accurate allelic reads counter. Bioinformatics. 2018 Apr 15; 34(8):1313-1320. Miao Z, Alvarez M, Pajukanta P, Ko A. PMID: 29186329; PMCID: PMC5905663.
Access ASElux Code on GitHub

Summary statistics of the MASLD score GWAS

Description: These are the summary statistics of the MASLD score GWAS data for our paper Miao Z, Garske KM, Pan DZ, Koka A, Kaminska D, Männistö V, Sinsheimer JS, Pihlajamäki J, Pajukanta P. Identification of 90 NAFLD GWAS loci and establishment of NAFLD PRS and causal role of NAFLD in coronary artery disease. HGG Adv. 2021; 3(1): 100056. PMID: 35047847.
Access the Data

Summary of subcutaneous adipose tissue (SAT) and liver cis-eQTL analysis

Description: These are the summary statistics of the adipose and liver bulk RNA sequencing (RNA-seq) cis-eQTL analysis from Matrix-eQTL for our paper Lee SHT, Garske KM, Arasu UT, Kar A, Miao Z, Alvarez M, Koka A, Darci-Maher N, Benhammou JN, Pan DZ, Örd T, Kaminska D, Männistö V, Heinonen S, Wabitsch M, Laakso M, Agopian VG, Pisegna JR, Pietiläinen KH, Pihlajamäki J, Kaikkonen MU, Pajukanta P. Single nucleus RNA-sequencing integrated into risk variant colocalization discovers 17 cell-type-specific abdominal obesity genes for metabolic dysfunction-associated steatotic liver disease. EBioMedicine. 2024;106:105232. PMID: 38991381.Access the Data

Genome-wide iHS statistics analysis

Description: These are the genome-wide iHS statistics in the Finnish METSIM cohort for our paper Deal M, Kar A, Lee SHT, Alvarez M, Rajkumar S, Arasu UT, Kaminska A, Männistö V, van der Kolk B, Säiläkivi U, Saarinen T, Juuti A, Pihlajamäki J, Kaikkonen MU, Laakso M, Pietiläinen KH, Pajukanta P. An abdominal obesity missense variant in the adipocyte thermogenesis gene TBX15 is implicated in adaptation to cold in Finns. Am J Hum Genet. 2024 Nov 7;111(11):2542-2560. PMID: 39515300; PMCID: PMC11568758.Access the Data