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scphaser – haplotype inference using single-cell RNA-seq data

scphaser – haplotype inference using single-cell RNA-seq data

Determination of haplotypes is important for modelling the phenotypic consequences of genetic variation in diploid organisms, including cis-regulatory control and compound heterozygosity. Karolinska Institute researchers realized that single cell RNA-seq (scRNA-seq) data is well suited for phasing genetic variants, since ...

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petal – Co-expression network modelling in R

petal – Co-expression network modelling in R

Networks provide effective models to study complex biological systems, such as gene and protein interaction networks. With the advent of new sequencing technologies, many life scientists are grasping for user-friendly methods and tools to examine biological components at the whole-systems ...

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PcircRNA_finder – circRNA prediction in plants

PcircRNA_finder – circRNA prediction in plants

Recent studies reveal an important role of non-coding circular RNA (circRNA) in the control of cellular processes. Because of differences in the organization of plant and mammal genomes, the sensitivity and accuracy of circRNA prediction programs using algorithms developed for ...

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SNP calling from RNA-seq data without a reference genome

SNP calling from RNA-seq data without a reference genome

SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot ...

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