Tag: heatmaps
Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects
Amino acid sequence comparisons between GAS and GBS Cas9 identify orthologous active sites Relationships between the amino acid sequence of GBS Cas9 endonuclease and its molecular functions can be deduced from detailed studies of its GAS ortholog, SpyCas9 (Supplementary Fig. 1). As a first step in locating DNA complementary to a…
Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and osteoarthritis
Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article CAS PubMed Google Scholar Puig-Junoy, J. & Ruiz Zamora, A. Socio-economic costs of osteoarthritis: A systematic review of cost-of-illness studies. Semin. Arthritis Rheum. 44, 531–541 (2015). Article PubMed Google Scholar Hunter, D. J., March, L. & Chew, M….
Tox4 regulates transcriptional elongation and reinitiation during murine T cell development
Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…
Italicise annotations with pheatmap
Hello, I have some column annotations in a heatmap (generated with pheatmap), which correspond to species that i want to be in italics. I have read through the pheatmap documentation and I can’t find anything. I have also tried to find and adapt solutions online (for example), but most tutorials…
Visualization App for RNASeq Differential Expression and Enrichment Analysis
Visualization App for RNASeq Differential Expression and Enrichment Analysis 0 Hello, I am looking to see what the latest and greatest is in terms of an app to visualize the results of a differential expression analysis of an RNASeq dataset, including any subsequent enrichment analyses. Ideally this app would take…
Pooled whole genome sequencing of the endangered Banff Springs Snail, Physella johnsoni, reveals genetic separation to P. gyrina and cryptic micro-geographical genetic structure
Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709. doi.org/10.1038/nrg2844 Article CAS PubMed Google Scholar Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. J Biol. doi.org/10.1186/jbiol60 Article PubMed PubMed Central Google Scholar Bickford D, Lohman DJ, Sodhi NS…
The RNA-DNA World And The Emergence Of DNA-encoded Heritable Traits
Origin & Evolution of Life Status Report biorxiv.org May 28, 2023 Stochastic simulation of a population of water-in-oil droplets containing strands. Heatmaps for A: average fraction of replicase ribozymes per droplet; B: fraction of droplets containing both replicase (R) and replicase encoding DNA template (TdR); C: average reaction propensity of…
IL5RA as an immunogenic cell death-related predictor in progression and therapeutic response of multiple myeloma
Differential expression analysis We downloaded GSE125361 (n = 48) microarray data from the Gene Expression Omnibus (GEO) database, which included 45 myeloma samples and 3 controls, for expression analysis of IL5RA in cancer16. Additionally, we analyzed the expression of IL5RA in smoldering myeloma (SMM) patients who progressed to active MM (n = 10) and…
Selective control of parasitic nematodes using bioactivated nematicides
Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260–20264 (2011). Article ADS CAS PubMed PubMed Central Google Scholar Hunter, M. C., Smith, R. G., Schipanski, M. E., Atwood, L. W. & Mortensen, D….
Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients
Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7. Article CAS PubMed Google Scholar Waldrop MP, Holloway JM, Smith DB, Goldhaber MB, Drenovsky RE, Scow KM, et al. The interacting roles of climate, soils, and…
Top 10 best Python Libraries for Data Science
Python Libraries for Data Science are the most used libraries in the Python programming world. Python has a wide range of libraries that provide functionality for data manipulation, analysis, visualization, and machine learning. In this blog post, we will discuss the top 10 Python libraries for data science. Python is…
Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1
Ethics approval and consent to participate The study was performed in accordance with the Guide for the Care and Use of Laboratory Animals of the US National Institutes of Health (NIH). The Seattle Children’s Research Institute (SCRI) has an Assurance from the Public Health Service through the Office of Laboratory…
Introduction to ggplot2 Package in R (Tutorial & Examples)
This tutorial demonstrates how to draw graphics using the ggplot2 package in R programming. The table of contents is shown below: So without further ado, let’s dig in… The Grammar of Graphics & ggplot2 Layers ggplot2 is a popular open-source data visualization package in R. It was created…
Normalizing RNA read counts for each gene?
Normalizing RNA read counts for each gene? 2 While reading a paper, I encountered the line “Heatmap of normalized read counts for chlorophyll-protein complexes (LHCs) normalized by row to reflect relative expression of each gene (see scale bar)” and was wondering if someone would be able to clarify how the…
Obtention of the binomial transformed count table with edgeR
Hello! When performing differential expression analysis with RNA-Seq data using DeSeq2, and after data normalisation, there is the option to extract a count table with the transformed abundance levels using the variance stabilisation transformation (vst) method. Line of code vst counts extraction: vst_dds <- vst(res) The DeSeq2 manual itself indicates…
Can I perform ANOVA test on rlog data of RNA sequencing counts?
Can I perform ANOVA test on rlog data of RNA sequencing counts? 0 Can I perform ANOVA test on rlog data of RNA sequencing counts? in order to see if the samples are different for example the cancer replicates from normal replicates? I did DESeq2, PCA, Heatmaps (Sample-distant matrix), Z-scores,…
Chan Zuckerberg ID Makes Strides in Enabling Pathogen Identification From Metagenomic Data
NEW YORK – A free, cloud-based data analysis platform to identify pathogens and other microbes from sequencing data dubbed Chan Zuckerberg ID (CZ ID) has been making inroads with infectious disease researchers around the world. The platform, developed by the Chan Zuckerberg Initiative and first released in 2019, recently added…
Comprehensive prediction of immune microenvironment and hot and cold tumor differentiation in cutaneous melanoma based on necroptosis-related lncRNA
Identify necroptosis-related lncRNAs in SKCM There are 386 necroptosis-related lncRNAs identified from the data of TCGA and GTEx, as the standard is the coefficients > 0.4 and P < 0.001. After that, flowing the differential expression analysis, 87 necroptosis-related lncRNAs were found to display significantly differential expression with the screen value as |logFC…
Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-‘omics analysis of the liver metabolic response to viral infection
Introduction The metabolome is an incredibly diverse collection of small molecules (<1,500 Da) in biological systems involved in virtually every cellular process, including cellular energy production, macromolecule synthesis, epigenetic modifications, cell signalling and more (for recent reviews see [Citation1–6]). It responds rapidly (in seconds) to both internal (signalling, allostery) and external…
A DBHS family member regulates male determination in the filariasis vector Armigeres subalbatus
Mosquitoes The Armigeres subalbatus GZ strain (Guangzhou Guangdong Province, China) was established in the laboratory in 2018 and reared in 30-cm3 nylon cages in the insectary at 28 ± 1 °C with 70–80% humidity and a 12:12 h (light: dark) light cycles. Larvae were fed with finely-ground fish food mixed 1:1 with yeast powder,…
Unveiling the Potential of CTGAN: Harnessing Generative AI for Synthetic Data
We all know that GANs are gaining traction in the generation of unstructured synthetic data, such as images and texts. However, very little work has been done on generating synthetic tabular data using GANs. Synthetic data has numerous benefits, including its use in machine learning applications, data privacy, data analysis,…
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…
Metatranscriptomic response of the wheat holobiont to decreasing soil water content
Soil water content (SWC) There was a significant difference (p = 0.000367) between the mean SWC across the four treatments. The water content was highest in plots exposed to 100% of the natural precipitation and gradually decreased in plots receiving 75%, 50% and 25% of the natural precipitation (Fig. 1A). The SWC was…
The Tip60/Ep400 chromatin remodeling complex impacts basic cellular functions in cranial neural crest-derived tissue during early orofacial development
Kat5-dependent alterations of gene expression in a cranial neural crest cell line To study the role of Kat5 in cells of the cranial neural crest, we first resorted to mouse O9-1 cells as a suitable and well characterized cellular model.18 In these cells, we used CRISPR/Cas9-dependent genome editing to inactivate…
is it possible to combine 4 heatmaps together?
Deseq2/ComplexHeatmap – is it possible to combine 4 heatmaps together? 0 I am working on a project that studies how gene expression may change across generations with repeated treatment. I have 5 generations that I’m looking at and each generation consists of 3 biological replicates for the control and the…
Is it possible to draw volcano plot without p values
Is it possible to draw volcano plot without p values 0 I have data like: I already draw heatmaps like: Is it possible to draw a volcano plot of this data without a p-value? plots p log2fold vaues • 116 views • link updated 2 hours ago by Basti ★…
heatmap issue
heatmap issue 1 i wanted to align my controls in one side and patients on the other side.. how can i do it? my code: heatmap(mat,cluster_rows = T, cluster_columns = T, column_lables=colnames(mat), name=”z-score”) heatmap DESeq2 • 56 views Your controls clearly show variable expression for the genes you’re plotting so…
The oncogenic properties of the EWSR1::CREM fusion gene are associated with polyamine metabolism
Knockdown of EWSR1::CREM and CREM expression in CHL-1 cell line induced senescence and reduced proliferation and migration Loss of EWSR1::CREM fusion protein in CHL-1 has previously been found to be associated with reduced proliferation, senescence and impaired invasion3. To validate these findings, we investigated the cellular properties associated with endogenous…
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
The 18-genome data package To investigate the genome inversion landscape of Asian rice from a population structure perspective, we first combined a set of 16 previously published high-quality genomes32,33,34 that represent the K = 15 population structure of O. sativa, plus the largest Xian/indica (XI) admixed subpopulation (XI-adm: Minghui 63 (MH63)) to…
Deeptools clustering differs when clustering sample as standalone and together with other samples
Deeptools clustering differs when clustering sample as standalone and together with other samples 0 Hi! I am using deepTools to generate heatmaps for different serine phosphorilations (ser2, ser5, ser7).I have observed a behavior that I don’t understand or I can’t explain, so maybe you could help me with it.I am…
Machine learning applications for the diagnosis, treatment and prognosis of cancer
Machine learning (ML) models have been increasingly used in clinical oncology for cancer diagnosis, outcome predictions, and informing oncological therapy planning. The early identification and prompt treatment of cancer, revolutionized by rapid and precise analysis of radiological and pathological images of tissues using ML algorithms, can improve the likelihood of…
BTEP Course: Data Visualization with R
When: April 11, 2023 – April 27, 2023 About this Course Welcome to the Data Visualization with R course series! Here, we hope to help you establish the foundations for generating publication quality plots in R. We will mostly be using ggplot2 (ggplot2.tidyverse.org/), a powerful yet easy to learn R package…
| EasyBiologyClass
Bioinformatics is an interdisciplinary field that analyzes and interprets biological data by combining biology, computer science, and statistics. There are various tools and techniques available for data analysis and interpretation. The software tools used in bioinformatics range from simple command-line utilities to more complex graphical programs and standalone web-services made…
Domain adaptation for supervised integration of scRNA-seq data
SIDA framework To achieve supervised integration, we propose to use a domain adaptation deep learning network architecture, which is able to incorporate cell type labels to inform data integration. As shown in Fig. 1, this network architecture takes training pairs generated by cells from different batches as input and passes the…
New technology maps where and how cells read their genome
Design and evaluation of spatial epigenome–transcriptome cosequencing with E13 mouse embryo. a, Schematic workflow. b, Comparison of number of unique fragments and fraction of reads in peaks (FRiP) in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. c, Gene and UMI count distribution in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. Number of pixels in…
Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli
Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004). Article CAS PubMed Google Scholar Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 142–201 (1998). Article CAS PubMed PubMed Central Google Scholar Croxen, M. A….
A Promising Technique for Identifying Fish Eggs and Monitoring Spawning Dynamics
Scientists have recently conducted a study, which has been published in the reputable journal PeerJ Life & Environment and featured in the International Association for Biological Oceanography Hub, to investigate the effectiveness of DNA metabarcoding in identifying fish eggs. The primary objective of this research was to evaluate the performance…
STING agonism turns human T cells into interferon-producing cells but impedes their functionality
. 2023 Mar 6;24(3):e55536. doi: 10.15252/embr.202255536. Epub 2023 Jan 27. Niklas Kuhl # 1 2 , Andreas Linder # 1 2 , Nora Philipp 1 3 , Daniel Nixdorf 1 3 , Hannah Fischer 1 , Simon Veth 4 , Gunnar Kuut 1 , Teng Teng Xu 1 3 , Sebastian Theurich 1 3…
Analysis of Molecular Mechanism between COPD and osteporosis
Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory condition that mostly occurs in middle-aged and elderly people. COPD manifests as a progressive airflow limitation associated with an abnormal lung inflammatory response.1 As a disease with high incidence, disability rate, long disease course, and multiple comorbidities, COPD has…
Assessing the risk of excess folic acid intake
Both high FA and low FA intake increases de novo mutation rate and disrupt genome DNA methylation in the offspring. a Violin Plot of DNSNV/DNM (de novo mutation) counts among the three different FA dietary groups (sample size for each group was as follows; combined panel: 0.3 ppm group n = 26;…
Transcription of MERVL retrotransposons is required for preimplantation embryo development
MERVL exhibits distinct localization in mouse embryos To understand the dynamics of MERVL expression, we first analyzed publicly available single-cell RNA-sequencing (scRNA-seq) datasets from each blastomere at eight representative stages of preimplantation development18 (Fig. 1a). To define regions of nonredundant MERVLs in mouse genome, we used RepeatMasker to annotate the…
Should I use TPM or TMM to plot gene expression boxplots in RNAseq?
Should I use TPM or TMM to plot gene expression boxplots in RNAseq? 0 Hi all! I used $TRINITY_HOME/util/align_and_estimate_abundance.pl from trinity to do transcript quantification for my RNAseq data. Then I got the following outputs: I would like to plot the boxplots for several genes. Which one should I use….
High-throughput microbial culturomics using automation and machine learning
Data-driven culturomics using phenotypes and automation Colony picking is a classic microbiology method for clonally isolating bacterial strains. Colony growth on plates depends on many factors, including the composition of the media (for example, available nutrients), atmospheric conditions (for example, level of oxygenation), presence of inhibitory molecules (for example, antibiotics),…
Co-diversification of an intestinal Mycoplasma and its salmonid host
Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 2016;31:689–99. Article PubMed Google Scholar Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28:12–22. Article CAS PubMed Google Scholar Alberdi A,…
Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks
Croft, M. T., Lawrence, A. D., Raux-Deery, E., Warren, M. J. & Smith, A. G. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature doi.org/10.1038/nature04056 (2005). Article PubMed Google Scholar Kazamia, E. et al. Mutualistic interactions between vitamin B12-dependent algae and heterotrophic bacteria exhibit regulation. Environ. Microbiol. doi.org/10.1111/j.1462-2920.2012.02733.x…
Identification and validation of BCL6 and VEGFA as biomarkers and ageing patterns correlating with immune infiltrates in OA progression
Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article CAS Google Scholar Hunter, D. J., March, L. & Chew, M. Osteoarthritis in 2020 and beyond: A Lancet Commission. Lancet 396, 1711–1712 (2020). Article Google Scholar Puig-Junoy, J. & RuizZamora, A. Socio-economic costs of osteoarthritis: A systematic review…
ggplot2 – Comparison between two different species with different gene, tissue names and number of tissues in R
I want to create 2,3 heatmaps or barcharts side by side for every gene ortholog between two or three different species in R. The problem is that my data are unbalanced, meaning I have gene names which are different between the two species (cat1_gene – mat1_gene) and tissues which are…
Human striatal glia differentially contribute to AD- and PD-specific neurodegeneration
Taylor, J. P., Hardy, J. & Fischbeck, K. H. Toxic proteins in neurodegenerative disease. Science 296, 1991–1995 (2002). Article CAS Google Scholar Spires-Jones, T. L., Attems, J. & Thal, D. R. Interactions of pathological proteins in neurodegenerative diseases. Acta Neuropathol. 134, 187–205 (2017). Article CAS Google Scholar Gan, L., Cookson,…
Molecular characterization of human cytomegalovirus infection with single-cell transcriptomics
Ethics statement All fresh peripheral blood samples were obtained after approval of protocols by the Weizmann Institutional Review Board (IRB application 92-1) and following informed consent from the donors. The study using BAL fluid samples was approved by the Hadassah Medical Organization research ethics committee in accordance with the Declaration…
Identification of key genes related to immune infiltration in cirrhosis via bioinformatics analysis
Lozano, R. et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380(9859), 2095–2128 (2012). Google Scholar Blachier, M., Leleu, H., Peck-Radosavljevic, M., Valla, D. C. & Roudot-Thoraval, F….
ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data
Generating mock metagenomic Hi-C datasets for benchmarking All viral contigs detected by VirSorter were assessed by CheckV to select single contigs with high completeness as putative reference genomes. As a result, 51 putative reference genomes, with length ranging from 11,410 bp to 194,784 bp were generated from the human dataset;…
GOplots::GOChord with heatmaps?
GOplots::GOChord with heatmaps? 0 @adrijakalvisa-22810 Last seen 16 hours ago Denmark Hi all, is there a way to add a gene expression heatmap option to GOplots::GOChord plot? Or multiple heatmaps at once? An example Chord plot: Fig 6 in PMID: 33674625. Here is what I tried: library(GOplot) data(EC) circ <-…
The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription
Boore, J. L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767–1780 (1999). Article CAS Google Scholar Calvo, S. E., Clauser, K. R. & Mootha, V. K. MitoCarta2. 0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res. 44, D1251–D1257 (2016). Article CAS Google Scholar Andrews, R. M. et al….
Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease
The heterogeneity of GABAergic neurons in human, macaque, mouse, and pig To perform a cross-species comparative study of the GABAergic neurons, we collected the snRNA-seq datasets of the cerebral cortex for human10,11, macaque12,13, mouse14,15, and pig16. After cell-type annotation and filtering out the excitatory neurons and non-neurons, the GABAergic neurons…
Multiplexed base editing through Cas12a variant-mediated cytosine and adenine base editors
Robust C-to-T conversion by Cas12a variant-mediated CBEs for non-canonical PAMs We initially attempted to screen for optimal cytosine deaminases that confer powerful C-to-T editing for Cas12a-mediated CBEs. Seven dCas12a-CBEs fused with individual cytosine deaminases1,2,16,20,21,22,24,25,26 were compared in HEK293T cells and porcine embryos at sites with TTTV PAM sequences. The dCas12a-A3A…
Insights on the bacterial composition of Parmigiano Reggiano Pure Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait
Smid, E. J. et al. Practical implications of the microbial group construction of undefined mesophilic starter cultures. Microb. Cell Factories 13, S2. doi.org/10.1186/1475-2859-13-S1-S2 (2014). Article Google Scholar Stadhouders, J. & Leenders, G. J. M. Spontaneously developed mixed-strain cheese starters. Their behaviour in direction of phages and their use within the…
Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing
Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. Kabuki make-up syndrome: a syndrome of mentalretardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J Pediatrics. 1981;99:565–9. CAS Article Google Scholar Kuroki Y, Suzuki Y, Chyo H, Hata A, Matsui I. A new malformation syndrome of long…
Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora
Choo, L. M., Niissalo, M. A., Leong, P. K. F. & Khew, G. S. The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae). Phytotaxa 458, 159–166 (2020). Nguyet, H. N. L. et al. An updated checklist of Theaceae and a new species…
Nanobody-based RFP-dependent Cre recombinase for selective anterograde tracing in RFP-expressing transgenic animals
Screening of efficient mCherry-binding protein (MBP) pairs to design Cre recombinase dependent on RFPs First, we aimed to construct Cre recombinase dependent on RFPs based on the reported tool named Cre-DOG30. In this system, N-terminal and C-terminal split Cre recombinase fragments are fused with specific nanobodies for target proteins, and…
Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3
In vitro reconstitution of Escherichia coli CRISPR-Cas3 interference E. coli CRISPR-Cas3 is generally well-characterized type I CRISPR complexes in vitro and in vivo32,33,37,38. However, recombinant EcoCas3 protein is difficult to purify because of poor solubility and propensity to aggregate at 37 °C25,26,30,39. Co-expression of HtpG chaperon40 and/or low temperature growth at…
NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis
NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…
Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth
Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…
bioconductor – Generating graphical results within from bioinformatics/nature genomics papers
I am a computational scientist with background in computer science and engineering however very new to the field of bioinformatics and computational genomics. Looking at papers in nature, PLOS, Cell, PNAS etc. within the topic of computational genomics, I see a very similar set of very sophisticated graphical results, ranging…
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…
Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host’s body temperature
From the bovine liver, we isolated 97 live F. hepatica adults. After overnight cultivation, we recovered approx. 228,000 laid eggs, which we divided in three groups. The first group (T0) was immediately frozen at − 80 °C, while the other two groups (T5 and T10) were incubated for 5 and 10 days at…
Bioconductor – ComplexHeatmap
DOI: 10.18129/B9.bioc.ComplexHeatmap This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…
Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani
Infection with L. donovani amastigotes or promastigotes promotes early changes in the mRNA pool of the host cell To compare the early effects of the two life stages L. donovani in the mature mRNA pool of the host cell, total cytosolic mRNA extracts from bone marrow-derived macrophage (BMDM) cultures infected…
Bioinformatics analysis identifies widely expressed genes
1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…
A Comprehensive Guide on ggplot2 in R
Image source: Author Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…
Secondary succession of bacterial communities and co-occurrence of phylotypes in oil-polluted Populus rhizosphere
doi.org/10.1016/j.soilbio.2012.11.018Get rights and content Abstract Oil pollution can be considered as a driver for bacterial secondary succession. A greenhouse study was conducted using forest mineral soil contaminated by heavy fuel oil and planted with hybrid aspen. The aim was to compare the bacterial succession in oil- and plant-amended ecosystems. Samples…
Validation of hub genes in acute pancreatitis
Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…
Introduction to ggplot2 with R – LibCal
Overview This is a hands-on workshop that covers how to use ggplot2 for common visualizations using the R programming language. It is not an introductory R programming workshop. See prerequisities below. Objectives In this workshop you will see how to use ggplot2 for: describing single variables and plotting simple…
nf-core/circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…
Bioinformatics Research Scientist (Blue Sky Initiative), Memphis, Tennessee
M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…
Bioconductor – DaMiRseq (development version)
DOI: 10.18129/B9.bioc.DaMiRseq This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…
Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics
1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed Google Scholar 2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed PubMed Central Google Scholar 3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….
an R package for interactive visualization of multi-omics data and annotation of chromosomes
Additional file 1. Example of chromoMap interactive plot constructed using various features of chromoMap including polyploidy (used as multi-track), feature-associated data visualization (scatter and bar plots), chromosome heatmaps, data filters (color-coded scatter and bars). Differential gene expression in a cohort of patients positive for COVID19 and healthy individuals (NCBI Gene…
Immune-related Prognostic Genes of ccRCC
Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…
Identification of differentially expressed genes in AF
Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…
Circos plot of dominant OTU with phylogenetic tree
Circos plot of dominant OTU with phylogenetic tree 0 I am trying to create a circos plot of dominant OTUs (from metagenomic data) with a phylogenetic tree inside the circle and the heatmaps around (like the attached image). Kindly suggest how can I achieve this using circos. Thank you. analysis…
miRNAs and mRNAs in intestinal ischemia-reperfusion injury
Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…
Creating Heatmaps Of Diffrentially Expressed Genes In Angilent Single-Color Array Analysis
Creating Heatmaps Of Diffrentially Expressed Genes In Angilent Single-Color Array Analysis 0 I am using limma to analyze Agilent’s single color arrays to find differentially expressed genes, using the following procedure. targets <- limma::readTargets(“targets.txt”) project <- limma::read.maimages(targets,source=”agilent”, green.only=TRUE) project.bgc <- backgroundCorrect(project, method=”normexp”, offset=50) project.NormData <-normalizeBetweenArrays(project.bgc,method=”quantile”) design <- paste(targets$Target, sep=””) design…
GitHub – MD-Anderson-Bioinformatics/EGFR-Structure-Function-Nature-Manuscript
These files contain the source data and code used for the analyses included in the publication Robichaux et al 2021, “Structure-based classification predicts drug response in EGFR mutant NSCLC” These files will be made public at the time of acceptance.The files include but are not limited to: Summary of EGFR…
How do I determine p-value and fold change for TMM normalized data?
How do I determine p-value and fold change for TMM normalized data? 0 Hi, I have a TMM normalized data for cancer vs no cancer treatment. This data, however, does not contain p-value or fold change. I want to generate plots such as heatmaps and volcano plots, but I cann’t…
Kaggle Mini Courses
Listing Results Kaggle mini courses Learn Python, Data Viz, Pandas & More Tutorials Kaggle Data Kaggle.com All Courses 8 hours agoPython Learn the most important language for data science. Intro to Machine Learning Learn the core ideas in machine learning, and build your first models. Intermediate Machine Learning Handle missing…
kaggle datasets for tableau
The homepage is full of small visualizations telling stories about each data set. This is the default Tableau location (if you’ve not changed) so far. Transformation processes can also be referred to as data wrangling, or data munging, transforming and mapping data from one raw data form into another format…
Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer
Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…
Advice on organizing large GSVA heatmap
Advice on organizing large GSVA heatmap 1 Hi there, I wanted to get some advice on how you might make your heatmap easier to read. In my case, I generated a heatmap from GSVA data which I filtered to only include significant pathways, here. I wanted to see how each…
R Programming – how to make a simple heat map
R Programming – how to make a simple heat map 5 Hi can anyone guide me how to make a simple heat map in R? Heatmap R • 264 views There is github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap…
R Programming
R Programming 4 Hi can anyone guide me how to make a simple heat map in R? in Heatmap R • 201 views There is github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap packages and want to have a consistent…