Tag: R

Lead Bioinformatics Data Scientist – Reed.co.uk

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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I can’t install the dplyr package on RStudio

I can’t install the “dplyr” package on RStudio. When I try, the following warnings appear: > install.packages(“dplyr”) Installing package into ‘C:/Users/elisa/Desktop/OneDrive/Documentos/R/win-library/3.4’ (as ‘ lib ‘ is unspecified) also installing the dependencies ‘ellipsis‘, ‘pillar’ ‘ ‘glue’ ‘ ‘lifecycle’,’ rlang‘,’ tibble‘,’ tidyselect‘,’vctrs ‘ There are binary versions available but the source versions…

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Run plotting code and view svg in RStudio Viewer or web…

R: Run plotting code and view svg in RStudio Viewer or web… dsvg_view {ggiraph} R Documentation Run plotting code and view svg in RStudio Viewer or web broswer. Description This is useful primarily for testing. Requires the htmltools package. Usage dsvg_view(code, …) Arguments code Plotting code to execute. … Other…

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Run plotting code and view svg in RStudio Viewer or web…

R: Run plotting code and view svg in RStudio Viewer or web… dsvg_view {ggiraph} R Documentation Run plotting code and view svg in RStudio Viewer or web broswer. Description This is useful primarily for testing. Requires the htmltools package. Usage dsvg_view(code, …) Arguments code Plotting code to execute. … Other…

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Immunotherapy for Diffuse Large B-Cell Lymphoma: Current Landscape and Future Directions

Review . 2021 Nov 20;13(22):5827. doi: 10.3390/cancers13225827. Affiliations Expand Affiliations 1 Department of Oncology, Barbara Ann Karmanos Cancer Institute, Wayne State University, 4100 John R, HW04HO, Detroit, MI 48201, USA. 2 Department of Hematology and Oncology, St Joseph Mercy Health System, Ann Arbor, MI 48201, USA. Item in Clipboard Review…

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130releng-armv7-quarterly][math/py-pymc3] Failed for py38-pymc3-3.11.4 in fetch

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/46aef99be2ae/logs/py38-pymc3-3.11.4.log Build URL: beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=46aef99be2ae Log: =>> Building math/py-pymc3 build started at Sat Nov 27…

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kubernetes openapi unmangler | RustRepo

A kubernetes openapi unmangler. Creates rust structs from a named crd by converting the live openapi schema. ⚠️ WARNING: ALPHA SOFTWARE ⚠️ Installation Grab a prebuilt musl/darwin binary from the latest release, or install from crates.io: Usage kopium prometheusrules.monitoring.coreos.com > prometheusrule.rs rustfmt +nightly –edition 2021 prometheusrule.rs Output use kube::CustomResource; use…

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DIRECTOR BIOINFORMATICS in Aliso Viejo California USA

Job Overview: The job’s main responsibility is to lead a bioinformatics team to collaborate with cross-functional departmental teams to build and integrate cutting edge computational solutions and applications to improve clinical diagnostics. With both technical and leadership capacities, the Director of Bioinformatics will drive bioinformatics strategy and initiatives in support…

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NEWS

NEWS Hopefully, finally fix compatibility with tidyeval changes in ggplot2 v2.3.0 Bug fixes Now actually compatible with ggplot2 v2.3.0 Major changes geom_gene_arrow() now supports forward aesthetic (#3 and #5, thanks geom_gene_label added (#3, thanks @adomingues) @adomingues and @jasonserviss) Compatible with ggplot2 v2.3.0 Minor changes Change R version dependency to fix…

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r – Adding three reference lines to a ggplot2 box plot works, but why can’t I add two reference lines?

I have an example data frame: #Libraries library(tidyverse) #Create example data ex <- data.frame(id = 1:300, event = rep(c(“f”, “s”, “t”), 100), x = rnorm(300, 50, 20)) And I need to make one plot with three horizontal reference lines and one plot with two horizontal reference lines. The plot with…

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r – phyloseq: Error in input$map_loaded : $ operator not defined for this S4 class

I am trying to make an NDMS plot with the plot_ordinate function in phyloseq and I keep getting this error. It worked for me previously. This is my code. dist <- phyloseq::distance(rf.indpig.decomp, method=”bray”) ordination <- ordinate(rf.indpig.decomp, method=”NDMS”, distance=dist) plot_ordination(rf.indpig.decomp, ordination, color=”decomp.stage”,shape=”location”) Error in input$map_loaded : $ operator not defined for…

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Bioconductor – Resourcerer

Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. Bioconductor version: 2.6 This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. Author:…

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Bioinformatics Software Engineer – Canton

Overview Abveris is Boston’s premier antibody discovery company providing contract research services to the biopharma industry. Abveris applies advanced immunization methods combined with B cell screening and hybridoma-based antibody discovery technologies to provide comprehensive gene-to-antibody discovery services. Abveris is developing the next generation of biologics, cell therapies, vaccines, and diagnostics…

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Bioinformatics Software Engineer – Canton

Overview Abveris is Boston’s premier antibody discovery company providing contract research services to the biopharma industry. Abveris applies advanced immunization methods combined with B cell screening and hybridoma-based antibody discovery technologies to provide comprehensive gene-to-antibody discovery services. Abveris is developing the next generation of biologics, cell therapies, vaccines, and diagnostics…

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Identifying Microbial Interaction Networks Based on Irregularly Spaced Longitudinal 16S rRNA sequence data

Abstract Though being vital for human health, microbial interactions with their host and with each other are still largely obscure for researchers. To deepen the understanding, the analyses based on longitudinal data are a better choice than the cross-sectional data since the information provided by the former is usually more…

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Identifying Microbial Interaction Networks Based on Irregularly Spaced Longitudinal 16S rRNA sequence data

Abstract Though being vital for human health, microbial interactions with their host and with each other are still largely obscure for researchers. To deepen the understanding, the analyses based on longitudinal data are a better choice than the cross-sectional data since the information provided by the former is usually more…

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ggplot2, aes vs aes_string

So I need to replace aes with aes_string due to failing rcmdcheck(). Original: aes( x = A, y = pmax(B, C, na.rm = TRUE), ), My confusion is regarding B and C. Am I allowed to put quotes around them since they are inside the pmax function? Like so: aes_string(…

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R Markdown for Mac M1 : RStudio

Search within r/RStudio Read more here: Source link

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Impact of protein conformational diversity on AlphaFold predictions

%PDF-1.4 % 125 0 obj > endobj 137 0 obj >stream Skia/PDF m97 Google Docs Renderer application/pdf Impact of protein conformational diversity on AlphaFold predictions 2021-11-27T16:08:55-08:00 2021-11-27T16:08:55-08:00 2021-11-27T16:08:55-08:00 uuid:16d62b69-1dd2-11b2-0a00-4c09271d5700 uuid:16d62b81-1dd2-11b2-0a00-bf0000000000 endstream endobj 124 0 obj > endobj 2 0 obj > endobj 62 0 obj > endobj 114 0 obj >…

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Bioinformatics Analyst II – Bethesda

PROGRAM DESCRIPTION The Advanced Biomedical Computing Center (ABCC) is a part of the Biomedical Informatics and Data Science (BIDS) Program at Leidos Biomedical Research, Inc. The ABCC provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff. KEY ROLES/RESPONSIBILITIES The…

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Construction of a circRNA-miRNA-mRNA Regulated Pathway Involved in EGFR-TKI Lung Adenocarcinoma Resistance

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

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Draw ggplot2 Plot with Factor Levels on X-Axis in R (Example)

  This article shows how to create a ggplot2 graphic with a factor on the x-axis in R programming. The tutorial consists of the following: Let’s dive right in…   Example Data & Packages The first step is to create some exemplifying data: data <- data.frame(group = factor(letters[1:5]), # Create…

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Grab Bag of GGplot2 Functions.

R: Grab Bag of GGplot2 Functions. ggallin-package {ggallin} R Documentation Grab Bag of GGplot2 Functions. Description This package consists of some helper functions for working with ggplot2: geoms, transforms, etc., with no real unifying theme among them. Legal Mumbo Jumbo ggallin is distributed in the hope that it will be…

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Bioconductor – edge

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see edge. Extraction of Differential Gene Expression Bioconductor version: 3.2 The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and…

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Bioconductor – topGO

topGO: Enrichment analysis for Gene Ontology Bioconductor version: 2.6 topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. Author: Adrian Alexa, Jorg…

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BIOINFORMATICS Job in California (CA), Career, Jobs in Aequor

Job Description The candidate will join a team focused on statistical model/data analysis/infrastructure developments for proteomics/lipidomics and collaboration with various scientific groups in ***, including bioinformatics and bench teams. This position provides the opportunity to implement and deliver bioinformatics tools for a wide range of applications. Key responsibilities:– Develop…

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r – ggplot2 two dataframes and two axes data not plotting

I have looked at similar questions and am trying to follow an example from a climate graph with temperature and precipitation. I am on the correct track, as both of the axes seem to have the correct limits. For some reason the bar graph of the proportion of the population…

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r – Unexpected color changes after upgrading to ggplot2 3.3.4

The picture shows the difference before and after upgrading ggplot2 from ver.3.3.3 to ver. 3.3.4 library(RColorBrewer) library(ggplot2) df <- structure(list(name = structure(c(11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,…

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r – Why ggplot can’t plot separate plots from this example from the r4ds book?

I am Learning R with the book R for Data Science 2017 – H.Wickham G.Grolemund I have a problem in the page 16 42/520. This is the code: ggplot(data = mpg) + geom_smooth(mapping = aes(x = displ, y = hwy)) ggplot(data = mpg) + geom_smooth(mapping = aes(x = displ, y…

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scikit learn – Miss-matching ROC and AUC calculations in python

I am currently using python to train a random forest model. I initially tried to compute the ROC curve representations as follows: import scikitplot as skplt from sklearn.metrics import RocCurveDisplay import sklearn from sklearn.ensemble import RandomForestClassifier from sklearn.model_selection import train_test_split from sklearn import metrics model2_bert = RandomForestClassifier(bootstrap=False, max_depth=None, max_features=”auto”, min_samples_leaf=5,…

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UniProtKB/SwissProt variant VAR_084499

Sequence information Variant position:  681 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  842 The length of the canonical sequence. Location on the sequence:   SLRSHIGVVPQDTVLFNDTI  A DNIRYGRVTAGNDEVEAAAQ The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_084499

Sequence information Variant position:  681 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  842 The length of the canonical sequence. Location on the sequence:   SLRSHIGVVPQDTVLFNDTI  A DNIRYGRVTAGNDEVEAAAQ The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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Importing GEO dataset

I need to import data GSE76124 in R studio the command I used is library(GEOquery) my_id <- "GSE76124" gse <- getGEO(my_id) the output and warning I'm getting is : Found 1 file(s) GSE76124_series_matrix.txt.gz trying URL 'ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76124/matrix/GSE76124_series_matrix.txt.gz&#039; Content type 'application/x-gzip' length 58695125 bytes (56.0 MB) ================================================== downloaded 56.0 MB Error: The…

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R: Main bedtools wrapper function.

R: Main bedtools wrapper function. tabix {bedr} R Documentation Main bedtools wrapper function. Description Main bedtools wrapper function. Usage tabix( region, file.name, params = NULL, tmpDir = NULL, deleteTmpDir = TRUE, outputDir = NULL, outputFile = NULL, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge…

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R: Main bedtools wrapper function.

R: Main bedtools wrapper function. tabix {bedr} R Documentation Main bedtools wrapper function. Description Main bedtools wrapper function. Usage tabix( region, file.name, params = NULL, tmpDir = NULL, deleteTmpDir = TRUE, outputDir = NULL, outputFile = NULL, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge…

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Bioinformatics Research Support

Bioinformatician – Research Support! London Paramount is working closely with a client who is now moving towards a future of enabling faster, deeper genomic research, bringing genomic healthcare to all who need it. They are looking for a Bioinformatician Research Support to join their amazing team in London. As a…

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Bioinformatics Research Support

Bioinformatician – Research Support! London Paramount is working closely with a client who is now moving towards a future of enabling faster, deeper genomic research, bringing genomic healthcare to all who need it. They are looking for a Bioinformatician Research Support to join their amazing team in London. As a…

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a deprecated ggplot2 theme developed for PDF and PNG for use…

R: a deprecated ggplot2 theme developed for PDF and PNG for use… theme_dpi {eeptools} R Documentation a deprecated ggplot2 theme developed for PDF and PNG for use at the Wisconsin Department of Public Instruction Description This is a custom ggplot2 theme developed for the Wisconsin Department of Public Instruction. This…

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r – Error in t.default(x) : argument is not a matrix

I am trying to see what people’s willingness to pay is for either nuclear or wind energy (far away or local) through a stated choice preference. I used the multinomial logit model, however when estimating the discreet choice for the different scenarios I keep getting an error: Error in t.default(x)…

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Stephen Sondheim, the Broadway legend, has died at 91

Composer and lyricist Stephen Sondheim in New York in 1976. Sondheim died on Friday at age 91. R. Jones / Getty Images Stephen Sondheim, the Pulitzer Prize- and Tony Award-winning Broadway songwriter died today at age 91, multiple media reports have confirmed. Sondheim would have been the first to tell…

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Stephen Sondheim, the Broadway legend, has died at 91

Composer and lyricist Stephen Sondheim in New York in 1976. Sondheim died on Friday at age 91. R. Jones / Getty Images Stephen Sondheim, the Pulitzer Prize- and Tony Award-winning Broadway songwriter died today at age 91, multiple media reports have confirmed. Sondheim would have been the first to tell…

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Bioconductor – SSPA

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SSPA. General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data Bioconductor version: 3.0 General Sample size and power analysis for microarray and next-generation sequencing data. Author: Maarten van Iterson Maintainer:…

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Bioconductor – CGHcall

Calling aberrations for array CGH tumor profiles. Bioconductor version: 2.6 Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. Author: Sjoerd Vosse and Mark van de Wiel Maintainer: Mark…

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NFP: Network fingerprint analysis in R

This package implements the network fingerprint framework. A biomedical network is characterized as a spectrum-like vector called “network fingerprint”, which contains similarities to basic networks. This knowledge-based multidimensional characterization provides a more intuitive way to decipher molecular networks, especially for large-scale network comparisons and clustering analyses Prerequisites NFP is free…

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r – RStudio, apply function by column class

I don’t have your data to verify that this will indeed work, but this dplyr solution should do it. library(dplyr) data %>% # the pipe operator makes this the first argument of the next function group_by(ens) %>% # groups by the ens variable so whatever happens next happens by group…

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multiple Rstudio sessions following the use of the parallel package

I’ve recently run into an issue when using Rstudio-Server that multiple sessions are spawned instead of a single session. In my case (see below) five sessions are created instead of one. This happens even after trying the normal solutions: deleting ~/.rstudio, clearing .GlobalEnv, and restarting R. Note, there is no…

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DNA Ancestral Marker Pedigree

1 HomoErectus hg38:21292569-T-G Human and Denisovan diverge from ancestral allele T found in chimpanzees at this position. hg38 Ref is G. 2 Heidelbergensis A8835 Presumed Y Ancestor of Humans and Neanderthals. ISOGG calls this haplogroup A000-T. 3 YAdam…

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Answer: vcftools 012 apparently is giving me wrong genotypes

If you are a Python user, below is a Python API solution using the `pyvcf` [submodule](https://sbslee-fuc.readthedocs.io/en/latest/api.html#module-fuc.api.pyvcf) from the `fuc` [package](https://sbslee-fuc.readthedocs.io/en/latest/readme.html) I wrote: Assume you have the following data: “` >>> from fuc import pyvcf >>> data = { … ‘CHROM’: [‘chr1’, ‘chr1’, ‘chr1’, ‘chr1’], … ‘POS’: [1076, 1114, 1128, 1202],…

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CRISPR AG (CRSP) falls 2.63% to Close at $78.79 on November 26

Last Price $ Last Trade Change $ Change Percent % Open $ Prev Close $ High $ low $ 52 Week High $ 52 Week Low $ Market Cap PE Ratio Volume Exchange CRSP – Market Data & News Trade CRISPR Therapeutics AG (NASDAQ: CRSP) shares fell 2.63%, or…

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Dry Lab Manager – Bioinformatics by Gold Group in Oxford, Oxfordshire Ref: 215263025

Dry Lab Manager – Bioinformatics Role My client is a biotechnology company developing RNA medicines. They are looking for a Dry Lab Manager for a growing Bioinformatics team. Ideally you will have a background in Bioinformatics and love all things tech including hardware, software, cloud, data and security. The Dry…

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A function to perform gene-level test using a sgRNA-level…

R: A function to perform gene-level test using a sgRNA-level… measure_gene_stats {CB2} R Documentation A function to perform gene-level test using a sgRNA-level statistics. Description A function to perform gene-level test using a sgRNA-level statistics. Usage measure_gene_stats(sgrna_stat, logFC_level = “sgRNA”) Arguments sgrna_stat A data frame created by ‘measure_sgrna_stats’ logFC_level The…

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The mtDNA mutation spectrum in the PolG mutator mouse reveals germline and somatic selection | BMC Genomic Data

1. Taylor RW, Turnbull DM. Mitochondrial DNA mutations in human disease [Internet]. Vol. 6, Nature Reviews Genetics. Europe PMC Funders; 2005 [cited 2020 Aug 21]. p. 389–402. Available from: /pmc/articles/PMC1762815/?report=abstract. 2. Kabunga P, Lau AK, Phan K, Puranik R, Liang C, Davis RL, Sue CM, Sy RW Systematic review of…

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B.Tech/M.Tech Fresher Bioinformatics and BioTech at Excelra Knowledge Solutions Private Limited India

Job Description Excelra is looking for Fresh B.Tech/ M.Tech graduates ( 2020 or 2021 pass outs) from Biotechnology/Bioinformatics/Biostatistics/Biomedical Engineering / Genetic Engineering Job description Responsibilities Utilize scientific expertise in areas of bioinformatics/Biotechnology and data science to produce scientific/business value and inform planning and decisions. Bring scientific understanding to bear on…

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Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location – /usr/local/lib/R/site-packages

Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location – /usr/local/lib/R/site-packages – is writable . · GitHub Instantly share code, notes, and snippets. Install R and RStudio on Ubuntu 18.04…

Continue Reading Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location – /usr/local/lib/R/site-packages

Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location – /usr/local/lib/R/site-packages

Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location – /usr/local/lib/R/site-packages – is writable . · GitHub Instantly share code, notes, and snippets. Install R and RStudio on Ubuntu 18.04…

Continue Reading Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location – /usr/local/lib/R/site-packages

Have a Software Design Idea? Kaggle Could Help It Happen for Free

In a recent Mind Matters podcast, “Artificial General Intelligence: the Modern Homunculus,” Walter Bradley Center director Robert J. Marks, a computer engineering prof, spoke with Justin Bui from his own research group at Baylor University in Texas about what’s happening — and isn’t happening — in artificial intelligence today. The…

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Have a Software Design Idea? Kaggle Could Help It Happen for Free

In a recent Mind Matters podcast, “Artificial General Intelligence: the Modern Homunculus,” Walter Bradley Center director Robert J. Marks, a computer engineering prof, spoke with Justin Bui from his own research group at Baylor University in Texas about what’s happening — and isn’t happening — in artificial intelligence today. The…

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UniProtKB/SwissProt variant VAR_084612

Sequence information Variant position:  430 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  797 The length of the canonical sequence. Location on the sequence:   DAVGRKRGRGNFGGQSEQEN  T LNQLLVEMDGFNTTTNVVIL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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B.1.1.529: How dangerous is the new variant found in South Africa?

By Adam Vaughan A woman in Johannesburg, South Africa, receives a nasal swab from a health worker EMMANUEL CROSET/AFP via Getty Images A new variant of SARS-CoV-2, known as B.1.1.529, with an unusually high number of mutations has been detected in South Africa and appears to have triggered a recent…

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Pulmonary Infection Revealed by Metagenomic NGS

1Department of Biomedical Engineering, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People’s Republic of China; 2Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People’s Republic of China Background: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by…

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What Are The Best Cities In Europe To Find Tech Jobs?

Now, there are plenty of jobs in tech whether it’s a full-on technology role or a supportive one in another industry. From technicians and operators, to IT support and software development, there are plenty of career opportunities that have been created thanks to the advancement of technology. In fact, the…

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Bioconductor – epistack (development version)

DOI: 10.18129/B9.bioc.epistack     This is the development version of epistack; for the stable release version, see epistack. Heatmaps of Stack Profiles from Epigenetic Signals Bioconductor version: Development (3.15) The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq,…

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Many SNPs getting excluded during PRSice 2 analysis

Many SNPs getting excluded during PRSice 2 analysis 1 Hello I am running PRSice 2, But there are many variants info which is not included during the process, My code, Rscript PRSice.R –prsice PRSice_linux –dir /home/projects/base-files/T2test/PRSice –base T2baseNoBMI.uniq.txt –target contn.analysis.PRS# –pheno T2.train.control60.txt –cov covariates.cont60.txt –binary-target T –snp rsID –chr CHR…

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Gradient-color a line in ggplot2 R

One option to achieve that would be via ggforce::geom_link2: library(ggforce) #> Loading required package: ggplot2 d <- tibble::tibble( `Country Name` = c(‘Estados Unidos’, ‘Estados Unidos’), `Country Code` = c(‘USA’, ‘USA’), Year = c(1961, 2020), `CrecimientoPBI (%)` = c(2.3, -3.49), `Inflación (%)` = c(1.07, 1.23), `Desempleo (%)` = c(6.7, 8.05) )…

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Gradient-color a line in ggplot2 R

One option to achieve that would be via ggforce::geom_link2: library(ggforce) #> Loading required package: ggplot2 d <- tibble::tibble( `Country Name` = c(‘Estados Unidos’, ‘Estados Unidos’), `Country Code` = c(‘USA’, ‘USA’), Year = c(1961, 2020), `CrecimientoPBI (%)` = c(2.3, -3.49), `Inflación (%)` = c(1.07, 1.23), `Desempleo (%)` = c(6.7, 8.05) )…

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A human fetal liver-derived infant MLL-AF4 acute lymphoblastic leukemia model reveals a distinct fetal gene expression program

This article was originally published here Nat Commun. 2021 Nov 25;12(1):6905. doi: 10.1038/s41467-021-27270-z. ABSTRACT Although 90% of children with acute lymphoblastic leukemia (ALL) are now cured, the prognosis for infant-ALL remains dismal. Infant-ALL is usually caused by a single genetic hit that arises in utero: an MLL/KMT2A gene rearrangement (MLL-r)….

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Development Scientist – Bioinformatics Job in Massachusetts

New England Biolabs (NEB) is seeking a computational scientist to work collaboratively with bench scientists. We will collaboratively construct software methods, analyze sequence results, and integrate data from instrumentation, ultimately creating high quality, rigorously tested, and provably excellent products. NEB provides an ideal working environment including high quality computational…

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The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

1. The Plant List. The Plant List—A Working List of All Plant Species (Royal Botanic Gardens, Kew and Missouri Botanical Garden, 2019). www.theplantlist.org/. Retrieved 20 Aug 2019. 2. Christenhusz, M. J. M. & Byng, J. W. The number of known plants species in the world and its annual increase. Phytotaxa…

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Keep rows with columns having values between -1 and 1 from a dataframe in R

Keep rows with columns having values between -1 and 1 from a dataframe in R 1 I have a dataframe in R that looks like this: V1 T1 T2 T3 T4 T5 CXCL6 0.8536601 1.0903336 3.7633042 5.5800459 5.8477150 PPBP 0.7739450 0.3587961 0.5073359 0.2743522 0.6221722 CXCL10 0.1258370 -0.3535165 -0.7460387 3.5604672 0.1971432…

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corral: Single-cell RNA-seq dimension reduction, batch integration, and visualization with correspondence analysis

Abstract Effective dimension reduction is an essential step in analysis of single cell RNA-seq(scRNAseq) count data, which are high-dimensional, sparse, and noisy. Principal component analysis (PCA) is widely used in analytical pipelines, and since PCA requires continuous data, it is often coupled with log-transformation in scRNAseq applications. However, log-transformation of…

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Bioconductor – HEM

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see HEM. Heterogeneous error model for identification of differentially expressed genes under multiple conditions Bioconductor version: 2.9 This package fits heterogeneous error models for analysis of microarray data Author: HyungJun Cho <hcho at virginia.edu>…

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pytorch implementation of openpose including Hand and Body Pose Estimation.

pytorch-openpose pytorch implementation of openpose including Body and Hand Pose Estimation, and the pytorch model is directly converted from openpose caffemodel by caffemodel2pytorch. You could implement face keypoint detection in the same way if you are interested in. Pay attention to that the face keypoint detector was trained using the…

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R-Studio 8.17 Build 180955

R-Studio is a family of powerful and cost-effective data recovery and undelete utilities. Empowered by the new unique data recovery technologies, it is the most comprehensive solution for data recovery from FAT12/16/32, NTFS, NTFS5 (created or updated by Windows 2000), and Ext2FS (LINUX file system) partitions. It functions on local…

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Chloranthus genome provides insights into the early diversification of angiosperms

Genome sequencing, assembly, and annotation Chloranthus spicatus has a genome size of 2.97 Gb (gigabases) based on K-mer analysis (Supplementary Fig. 2, Supplementary Data 1); the individual sequenced had a heterozygosity rate of 0.99%, which is possibly associated with the obligate outcrossing system of this species31. Genomic DNA was sequenced using three different…

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Trying to pull some data from BigQuery into RStudio that is running on a Google Cloud Platform VM but not getting anything out, can someone help ! : googlecloud

So I installed RStudio on the GCP marketplace and accessed it online, installed readr package and bigrquery package, instantly im just trying to get it to show anything within R. I’m really new to the platforms mentioned above, here is the code im using: #library(bigrquery) project <- “TestConnectRToBigQuery” sql <-…

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ODE in RStudio, incorrect “variable does not exist” diagnostic error message – #3 by Tim_Tinker – Modeling

Hello, I am using cmdstan “2.28.1”, R version 4.1.1 and Rstudio 2021.09.0 Build 351 on Windows 64. In coding up a predator-prey model (with a custom user function called “dy_dt”) and using the new ODE functions (ode_rk45), I noticed that the Rstudio diagnostics flagged an error at the line where…

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ODE in RStudio, incorrect “variable does not exist” diagnostic error message – #3 by Tim_Tinker – Modeling

Hello, I am using cmdstan “2.28.1”, R version 4.1.1 and Rstudio 2021.09.0 Build 351 on Windows 64. In coding up a predator-prey model (with a custom user function called “dy_dt”) and using the new ODE functions (ode_rk45), I noticed that the Rstudio diagnostics flagged an error at the line where…

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LeftAlignIndels error

LeftAlignIndels error 0 Hello! I input sorted and indexing bam file to LeftAlignIndels: ~/Soft/gatk-4.1.9.0/gatk LeftAlignIndels -I bam_fin/Exome_dups.bam -R /mnt/lapd/Index_hum/dna2/GRCh_2021.fa -O bam_fin/Exome.bam And have this error: ‘java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment for file:///mnt/lapd/Vika_data/RNF_raw/exome/bam_fin/Exome.bam. Sort order is coordinate. Offending records are at [1:152985370] and [1:152985347] at htsjdk.samtools.SAMFileWriterImpl.assertPresorted(SAMFileWriterImpl.java:197) at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:184)…

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Download urlopener.exe RStudio

GamesConvertersRecoveryPicturesFile driversCodecsAntivirusesPlayersMakersRecordersDLLs Websites File name: urlopener.exeFile size: 4.22 mb.Date: 18.07.2016 18:40 Virus scan: download4.22 mb. urlopener.exe free download.If you receive an error urlopener.exe missing:– You can try to download this file and paste it in directory where it missingIf you receive an error in file urlopener.exe:– Try to replace it…

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Download urlopener.exe RStudio

GamesConvertersRecoveryPicturesFile driversCodecsAntivirusesPlayersMakersRecordersDLLs Websites File name: urlopener.exeFile size: 4.22 mb.Date: 18.07.2016 18:40 Virus scan: download4.22 mb. urlopener.exe free download.If you receive an error urlopener.exe missing:– You can try to download this file and paste it in directory where it missingIf you receive an error in file urlopener.exe:– Try to replace it…

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question about TCGA survival data

question about TCGA survival data 3 Many TCGA samples have three rows in their clinical data that may be of interest for survival analysis: days to death, days to last follow-up, and days to sample procurement. My questions are, in this data, what does day 0 refer to, and what…

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Bioconductor – nudge

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see nudge. Normal Uniform Differential Gene Expression detection Bioconductor version: 2.9 Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the…

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Bioconductor – xtropicaliscdf

DOI: 10.18129/B9.bioc.xtropicaliscdf     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see xtropicaliscdf. xtropicaliscdf Bioconductor version: 3.13 A package containing an environment representing the X_tropicalis.cdf file. Author: The Bioconductor Project Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“xtropicaliscdf”)):…

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Bioconductor – rgu34cprobe

DOI: 10.18129/B9.bioc.rgu34cprobe     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rgu34cprobe. Probe sequence data for microarrays of type rgu34c Bioconductor version: 3.10 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from www.affymetrix.com. The…

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Bioconductor – geneplotter

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see geneplotter. Graphics related functions for Bioconductor Bioconductor version: 2.9 Some basic functions for plotting genetic data Author: R. Gentleman, Biocore Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“geneplotter”)):…

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Main plot function for a ‘deepdep’ object

plot_dependencies {deepdep} R Documentation Main plot function for a deepdep object Description Visualize dependency data from a deepdep object using ggplot2 and ggraph packages. Several tree-like layouts are available. Usage plot_dependencies( x, type = “circular”, same_level = FALSE, reverse = FALSE, label_percentage = 1, show_version = FALSE, show_downloads = FALSE,…

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Bioconductor – pint

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see pint. Pairwise INTegration of functional genomics data Bioconductor version: 2.9 Pairwise data integration for functional genomics. In particular, tools to screen functionally active chromosomal aberrations from paired copy number, gene expression and miRNA…

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Bioconductor – pint

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see pint. Pairwise INTegration of functional genomics data Bioconductor version: 2.9 Pairwise data integration for functional genomics. In particular, tools to screen functionally active chromosomal aberrations from paired copy number, gene expression and miRNA…

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Bioinformatics Scientist at Infectious Disease Institute

IDI seeks to hire a Bioinformatics Scientist (BS) for the centre. The BS will be a fulltime staff who is familiar with the application of computational and biotechnology capabilities to biomedical and public health problems like genetics, clinical and medical research, as well as other data intensive analyses. By coordinating…

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Job details – Public Sector Resourcing

Job details – Public Sector Resourcing Home Job search FULL_TIME 2021-12-02 00:00:00 2021-11-25 Environmental Bioinformatics Researcher (Inside IR35) | Ref: PSR0024505 Remote/Home | Technology | Start: ASAP | Duration: 4 months Posted 23 hours ago Job description Contract Term: Until 31/03/2022 Contracting Authority: UK Health Security Agency Location: Remote Imagine…

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KEGG pathway modules

KEGG pathway modules 0 Hi everyone, I’m looking to create a table with in the first column genes (ENSEMBL ID or symbol) and in the second column all the pathway modules in which the gene is involved. For example this should be the result: | Gene 1 | module 1,…

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Inconsistent panel border width when exporting as SVG with Cairo

I am generating figures for a paper in svg format, and when I export the ggplot to .svg, I obtain inconsistent panel border widths depending on the device I use to export. I need to use CairoSVG as some figures have symbols that the standard device does not generate properly….

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R-Studio 8.17 Build 180955 (x64) Network Multilingual / AvaxHome

R-Studio 8.17 Build 180955 (x64) Network Multilingual | 64.2 Mb Empowered by the new unique data recovery technologies, R-STUDIO is the most comprehensive data recovery solution for recovery files from NTFS, NTFS5, ReFS, FAT12/16/32, exFAT, HFS/HFS+ (Macintosh), Little and Big Endian variants of UFS1/UFS2 (FreeBSD/OpenBSD/NetBSD/Solaris) and Ext2/Ext3/Ext4 FS (Linux) partitions….

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r – Git tab missing in RStudio after git installed on Windows

Installed R, R Studio, Git but when I opened R Studio, there was no Git tab, like the screenshot below:Windows 8.1, x64R version: 3.5.1R Studio version: 1.1.463Git: 2.19.2 When I opened Tools/Global Options/GitSVN:Git executable: C:/Program Files/Git/bin/git.exeSVN executable: C:/Program Files/Git/bin/sh.exe* I cannot find any file called “svn.exe” in the git folder….

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