Tag: pseudotime

Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis

Wang, J., Garancher, A., Ramaswamy, V. & Wechsler-Reya, R. J. Medulloblastoma: from molecular subgroups to molecular targeted therapies. Annu. Rev. Neurosci. 41, 207–232 (2018). Article  CAS  PubMed  Google Scholar  Cavalli, F. M. G. et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell 31, 737–754.e736 (2017). Article  CAS  PubMed  PubMed Central …

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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….

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Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020). CAS  PubMed  PubMed Central  Google Scholar  Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen…

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DESeq2 pseudotime series design?

DESeq2 pseudotime series design? 1 @jordiplanells-19865 Last seen 22 hours ago Sweden Hi all. First things first, sorry for posting one more question about experimental design and time series in DESeq2.We have performed RNA-seq with two different treatments (control and protein over-expression) in two different time points (t=0 and t=8h)….

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Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

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Which trajectory method is better !?

Which trajectory method is better !? 2 Hello I was engaged with a basic problem. I have dataset consist ~2000 cells and composed 8-9 clusters using Seurat package, then I transfer Seurat object to the Monocle. I tried monocle2 and monocle3. The problem is, how to make the trajectory ?…

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Extract root(start) and leaf(end) states programmatically in monocle2

Extract root(start) and leaf(end) states programmatically in monocle2 0 Dear bioinformaticians, do you know how to extract starting state and end states from the CDS in monocle2 ? I know I can detect them visually inspecting the States plot after I compute the pseudotime. I am asking if there is…

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Trouble running Cyclum for my scRNA-seq analysis

I have been analyzing some mouse T cell scRNA-seq data for a few months now using mostly the Seurat pipeline run with default parameters, and I have noticed that regressing out the ‘S.Score’ and ‘G2M.Score’ obtained from default Seurat::CellCycleScoring seems to be insufficient to remove (seemingly large) variation originating from…

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Bioconductor – traviz (development version)

DOI: 10.18129/B9.bioc.traviz     This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…

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heatmap of genes pseudotime in monoclle3

heatmap of genes pseudotime in monoclle3 0 Login before adding your answer. Traffic: 1946 users visited in the last hour Source link

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