eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale
10.1093/molbev/msab293 · doi-reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · doi-reference
Genetic association testing using the GENESIS R/Bioconductor package
10.1093/bioinformatics/btz567 · doi-reference
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
10.1093/bioinformatics/bts163 · doi-reference
The ade4 package: implementing the duality diagram for ecologists
10.18637/jss.v022.i04 · doi-reference
A unifying tool for linear multivariate statistical methods: the RV-coefficient
10.2307/2347233 · doi-reference
PROTEST: a PROcrustean randomization TEST of community environment concordance
10.1080/11956860.1995.11682297 · doi-reference
Controlling the false discovery rate: a practical and powerful approach to multiple testing
10.1111/j.2517-6161.1995.tb02031.x · doi-reference
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
10.1186/gb-2012-13-10-r87 · doi-reference
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
10.1093/bioinformatics/btw313 · doi-reference
10.1007/978-3-319-24277-4
10.1007/978-3-319-24277-4 · doi-reference
A high-performance computing toolset for relatedness and principal component analysis of SNP data
10.1093/bioinformatics/bts606 · doi-reference
Efficient methods to compute genomic predictions
10.3168/jds.2007-0980 · doi-reference
PLINK: a tool set for whole-genome association and population-based linkage analyses
10.1086/519795 · doi-reference
Second-generation PLINK: rising to the challenge of larger and richer datasets
10.1186/s13742-015-0047-8 · doi-reference
Genotype imputation with millions of reference samples
10.1016/j.ajhg.2015.11.020 · doi-reference
The variant call format and VCFtools
10.1093/bioinformatics/btr330 · doi-reference
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
10.1093/bioinformatics/btr167 · doi-reference
The Sequence Alignment/Map format and SAMtools
10.1093/bioinformatics/btp352 · doi-reference
10.1093/gigascience/giab008
10.1093/gigascience/giab008 · doi-reference
Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · doi-reference
1000 conifer genomes: Genome innovation, organisation and diversity
10.21203/rs.3.rs-6502828/v1 · doi-reference
MultiQC: summarize analysis results for multiple tools and samples in a single report
10.1093/bioinformatics/btw354 · doi-reference
Design and evaluation of a large sequence-capture probe set and associated SNPs for diploid and haploid samples of Norway spruce (Picea abies)
10.1101/291716 · doi-reference
Uncovering epigenetic and transcriptional regulation of growth in Douglas-fir: identification of differential methylation regions in mega-sized introns
10.1111/pbi.14229 · doi-reference
Epitype-inducing temperatures drive DNA methylation changes during somatic embryogenesis in the long-lived gymnosperm Norway spruce
10.3389/fpls.2023.1196806 · doi-reference
Cytokinin: from autoclaved DNA to two-component signaling
10.1093/plcell/koad327 · doi-reference
Targeted bisulfite sequencing of Scots pine adaptation-related genes
10.1016/j.plantsci.2024.112173 · doi-reference
Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing
10.1002/ece3.4374 · doi-reference
Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients
10.1111/mec.13563 · doi-reference
Epigenetics in forest trees: state of the art and potential implications for breeding and management in a context of climate change
10.1016/bs.abr.2018.09.003 · doi-reference
Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulated by rainout shelters
10.1111/plb.12049 · doi-reference
Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce
10.1111/eva.12801 · doi-reference
Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies
10.1038/hdy.2009.16 · doi-reference
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
10.1186/s13059-021-02392-1 · doi-reference
Epigenome plasticity in plants
10.1038/s41576-021-00407-y · doi-reference
10.1073/pnas.1215380110
10.1073/pnas.1215380110 · doi-reference
Gene body DNA methylation in plants
10.1016/j.pbi.2016.12.007 · doi-reference
10.1073/pnas.1604666113
10.1073/pnas.1604666113 · doi-reference
Advances and promises of epigenetics for forest trees
10.3390/f11090976 · doi-reference
