Contact information

Sampsa Hautaniemi, Prof.

Biomedicum Helsinki, B524b
P.O.Box 63 (Haartmaninkatu 8)
00014 UNIVERSITY OF HELSINKI
phone +358 2941 25419

firstname.lastname@helsinki.fi

Twitter @HautaniemiLab


Affiliations

 

Software developed in the lab

Andurilanduril figure
Anduril (ANalysis of Data Using Rapid Integration of aLgorithms) is an opensource component-based workflow framework for systematic, flexible and efficient scientific data analysis, particularly in the field of high-throughput experiments in biomedical research. It includes components for expression, SNP, ChIP-seq and exon microarray analysis.
[software] [abstract]

animaAnima
Anima is an image analysis workflow platfrom built on top of Anduril. Anima acts as a superplatform for the existing imaging applications, and can run components and software written many languages. In addition Anima provides API to the popular batch imaging environments: Fiji, CellProfiler and ImageMagick.
[software] [abstract]


CANGES
CANGES (Candidate Genes and SNPs) is a systematic data integration method that links SNP and linkage disequilibrium data to pathway- canges figureand protein-protein interaction information. It can be used as a knowledge discovery tool for the search of disease associated causative variants from genome-wide studies as well as to generate new hypotheses on synergistically functioning genes.
[abstract]CNAmet equation

CNAmet
CNAmet is an algorithm and R package that facilitates the integration of copy number, methylation and expression data. In addition to the CNAmet algorithm, our R package includes the S2N algorithm for the integration of copy number to expression data.
[software] [abstract]

CohortComparatorCohortCOmparator figure
CohortComparator is a SNP data analysis tool that can be used to identity candidate genes for recessive genotypes.
[abstract]

CsblGO figureCsbl.go
Csbl.go is an R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The package also includes GO enrichment analysis functionality.
[software] [abstract]


FlowAndFlowAnd figure
FlowAnd is designed to analyze and integratelargescale, multi-color flow cytometry data. It implements methods for data importing, various transformations, several clustering algorithms for automatic clustering, visualization tools as well as straightforward statistical testing.
[sofware] [abstract]

GROKcircos figure
GROK (Genomic Region Operation Toolkit) is "Swiss Army knife" library for processing genomic interval data. GROK operates ongenomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations.
[software] [abstract]

MEAP
MEAP (Multiple Exon Array Preprocessing) is an R package for large-scale exon array data analysis. It includes a novel algorithm (PM-BayesBG) to estimate sequence-based backgrounds that allows more reliable expression estimation than the existing background correction methods. MEAP also contains algorithms for generating robust expression estimates at exon, alternatively spliced variant and gene levels that facilitates the quantitative analysis of alternative spliced variants in the wholetranscriptome.
[software]

meap equation

Moksiskaan
moksiskaan figureMoksiskaan is a generic database that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. Moksiskaan provides various pathway components for Anduril and may be used to extends its capabilities.
[software] [abstract]

phoMSVal figurephoMSVal
phoMSVal is an open-source platform developed for managingMS/MS data andautomatically validating identified phosphopeptides. phoMSVal imports data into a MySQL relational database, extracts features for classification, and assigns a classification label to each spectrum designating whether the given peptide assignment is likely to be correct. The classifier used is a random forest classifier with an input of ten features calculated from the spectra.
[abstract] pina figure

PINA
PINA is an integrated platform for protein-protein interaction network construction, filtering, analysis, visualization and management.
[abstract]