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10 results for “redundancy analysis”
Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
<p><span>The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore the molecular basis of pigmentation variation in brown trout (<em>Salmo</em> <em>trutta</em>) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait GWAS allowed us to extract 337 independent "colour patterning loci" (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (<em>i</em>) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (<em>ii</em>) were found associated with</span><span> 218 </span><span>candidate genes, including 197 genes </span><span>formerly mentioned in the literature dealing with skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (<em>Onchorhynchus</em> <em>mykiss</em>)</span><span>, and (<em>iii</em>) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.</span></p>
Land-use change erodes trophic redundancy in tropical forest streams: Evidence from amino acid stable isotope analysis
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Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
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Replication Package for: "Redundancy-free Analysis of Multi-revision Software Artifacts"
<p>Researchers often analyze several revisions of a software project to obtain historical data about its evolution. For example, they statically analyze the source code and monitor the evolution of certain metrics over multiple revisions. The time and resource requirements for running these analyses often make it necessary to limit the number of analyzed revisions, e.g. by only selecting major revisions or by using a coarse-grained sampling strategy, which could remove significant details of the evolution. Most existing analysis techniques are not designed for the analysis of multi-revision artifacts and they treat each revision individually. However, the actual difference between two subsequent revisions is typically very small. Thus, tools tailored for the analysis of multiple revisions should only analyze these differences, thereby preventing re-computation and storage of redundant data, improving scalability and enabling the study of a larger number of revisions. In this work, we propose the Lean Language-Independent Software Analyzer (LISA), a generic framework for representing and analyzing multi-revisioned software artifacts. It employs a redundancy-free, multi-revision representation for artifacts and avoids re-computation by only analyzing changed artifact fragments across thousands of revisions. The evaluation of our approach consists of measuring the effect of each individual technique incorporated, an in-depth study of LISA's resource requirements and a large-scale analysis over 7 million program revisions of 4,000 software projects written in four languages. We show that the time and space requirements for multi-revision analyses can be reduced by multiple orders of magnitude, when compared to traditional, sequential approaches.</p>
FIGURE 2. Individual hypothetical area cladograms and matrix creation through BuM 2.0. A. Individual area cladogram with a redundant Area E. B. Individual area cladogram with a redundant Area D. C. Individual area cladogram with a in BuM 2.0: Software for online generation of matrices for Brooks Parsimony Analysis
FIGURE 2. Individual hypothetical area cladograms and matrix creation through BuM 2.0. A. Individual area cladogram with a redundant Area E. B. Individual area cladogram with a redundant Area D. C. Individual area cladogram with a MAST (D#E). D. Combined MRP-matrix after BuM 2.0 (option Modified BPA); og: outgroup. E. General area cladogram after the parsimony analysis of the combined matrix. The resulting pattern converges with the actual pattern of fragmentation of ancestral Area 0.
FIGURE 6. Redundancy Analysis biplot ordination diagram, obtain from a in The recognition of infraspecific taxa in Juniperus brevifolia (Cupressaceae)
FIGURE 6. Redundancy Analysis biplot ordination diagram, obtain from a matrix of 12 populations and 10 abiotic variables (not all variables are shown) (Abbreviations: see Table 1) (adapted from Elias 2007).
FIGURE 1. Redundancy Analysis biplot ordination diagram, obtain from a in The recognition of infraspecific taxa in Juniperus brevifolia (Cupressaceae)
FIGURE 1. Redundancy Analysis biplot ordination diagram, obtain from a matrix of 12 populations and 17 morphological variables (not all variables are shown) (Abbreviations: see Table 1) (adapted from Elias 2007).
Data from: Evaluation of redundancy analysis to identify signatures of local adaptation
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Analysis of redundancy between RNAi and piRNA pathways in the mouse oocytes
GEO Series GSE132121. Mus musculus. 22 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis reveals determinants of redundant and specific binding within a transcription factor family
GEO Series GSE7449. Homo sapiens. 36 samples. Type: Genome binding/occupancy profiling by genome tiling array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.