Category: github

Labelling SNPs in a stacked manhattan plot with karyoploteR

Labelling SNPs in a stacked manhattan plot with karyoploteR 0 When combining multiple GWAS results into a stacked manhattan plot using KaryoploteR, how do you label top SNPs in each set of GWAS results? Instructions provided for labelling a single manhattan plot did not work for the stacked manhattan. manhattan…

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Mouse RefCDS for dNdScv package

Mouse RefCDS for dNdScv package 0 Hi all I am trying to run the dNdScv package to identify mutations that are under positive selection. The dataset I am working with is sequencing data from mouse tumours using a targeted gene panel. The default for the package is using human data….

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About Foreign Fields in VCF (4.3)

About Foreign Fields in VCF (4.3) 0 I was looking at the VCF format 4.3 here – page 7 and 4.2 page 4. More or less they are similar, stating 8 mandatory and fixed, tab delimited columns. I was bit lost about the term ‘fixed’, I am wondering, say for…

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Computational Biology Trainer for VIB and ELIXIR Belgium

Description Posted Date 18 Oct 2021 Locations Ghent Center VIB Bioinformatics Core Type Bio IT Positions 1 About VIB and ELIXIR Belgium VIB is an entrepreneurial non-profit research institute with a clear focus on ground-breaking strategic basic research in life sciences and operates in close partnership with the five universities…

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how to map Pacbio CCS fastq

how to map Pacbio CCS fastq 1 I have a Pacbio CCS fastq like this I want to map to genome, and this is my command and out. I want to know how to solve it. Is this fastq correct? Thanks minimap2 Pacbio • 25 views It might pay to…

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11th Place Solution of Kaggle Global Wheat Detection

Solution Summary Our solution is based on the excellent MMDetection framework. We trained an ensemble of the following models: To increase the score a single round of pseudo labelling was applied to each model. Additionally, for a much better generalization of our models, we used heavy augmentations. Jigsaw puzzles In…

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ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files

GitHub – ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time About Wrapper script for a GenePattern module to create a velocity compatible loom file…

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Runs of homozygosity in Plink

❯ plink1.9 –homozyg –help PLINK v1.90b6.22 64-bit (3 Nov 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 –help present, ignoring other flags. –homozyg [{group | group-verbose}] [‘consensus-match’] [‘extend’] [‘subtract-1-from-lengths’] –homozyg-snp <min var count> –homozyg-kb <min length> –homozyg-density <max inverse density (kb/var)> –homozyg-gap <max internal gap…

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bcftools mpileup before bcftools call

bcftools mpileup before bcftools call 1 I want to variant call using bcftools call. However, when researching, I see a lot of people running bcftools mpileup before doing the actual variant calling with call. For example (from here): bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf…

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Tech-i-s/techis-ds-kaggle-sentiment_analysis_movie_review_NLP: Kaggle Sentiment analysis of movie review using Natural Language Processing Project

Classify the sentiment of sentences from the Rotten Tomatoes dataset Go to Page… “There’s a thin line between likably old-fashioned and fuddy-duddy, and The Count of Monte Cristo … never quite settles on either side.” The Rotten Tomatoes movie review dataset is a corpus of movie reviews used for sentiment…

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Error due to Sam to Bam and Indexing using picard

Error due to Sam to Bam and Indexing using picard 0 Hii all, I ran the following command: picard SortSam -I 10100123749_NIKEC.bam -O 10100123749.bam –SORT_ORDER coordinate –MAX_RECORDS_IN_RAM 1500000 –VALIDATION_STRINGENCY LENIENT But I am getting this error: 18:09:18.048 INFO NativeLibraryLoader – Loading libgkl_compression.so from jar:file:/home/mdrcubuntu/anaconda3/envs/smruti/share/picard-2.26.3-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Oct 18 18:09:18 IST 2021]…

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UCD Bioinformatics Core Workshop

Prepare your environment for Monocle Create an RStudio project In the R console run the following commands to install the needed packages to run Monocle3 if (!any(rownames(installed.packages()) == “remotes”)){ if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“remotes”) } library(remotes) if (!any(rownames(installed.packages()) == “Seurat”)){ BiocManager::install(“Seurat”) } library(Seurat) if (!any(rownames(installed.packages()) == “R.utils”)){ BiocManager::install(“R.utils”)…

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Bioconductor/EuroBioC2022: European Bioconductor conference website 2022

GitHub – Bioconductor/EuroBioC2022: European Bioconductor conference website 2022 Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time This repository contains material for the European Bioconductor annual conference. View the conference web site Make sure Hugo is installed. Check hugo version Clone the repository and…

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trimming fastq files

trimming fastq files 1 I have the fastq files of the data I want to trim. In the FastQC I saw that Nextera adapters were present in my sample. I saw few tutorials and it required to copy the sequences to the current directory so this was the command I…

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FeatureReader – htsjdk 1.133 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.133 javadoc.io/doc/com.github.samtools/htsjdk/1.133 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.133/package-list Read more here: Source link

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BamIndexValidator.IndexValidationStringency – htsjdk 2.2.2 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.2.2 javadoc.io/doc/com.github.samtools/htsjdk/2.2.2 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.2.2/package-list Read more here: Source link

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why Unable to establish SSL connection

why Unable to establish SSL connection 0 I want to install UCSC The Genome Browser in the Cloud (GBiC) on the server. After typing sudo bash browserSetup.sh install I get the following error –2021-10-18 10:19:21– raw.githubusercontent.com/paulfitz/mysql-connector-c/master/include/my_config.h Resolving raw.githubusercontent.com (raw.githubusercontent.com)… 185.199.110.133, 185.199.109.133, 185.199.111.133, … Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443… connected. Unable to…

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gromacs-plumed | MacPorts

Molecular dynamics package designed for simulations of proteins, lipids, and nucleic acids.: (THIS PORT INSTALLS A VERSION OF GROMACS PATCHED WITH PLUMED) GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed…

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Bioconductor – target

DOI: 10.18129/B9.bioc.target     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see target. Predict Combined Function of Transcription Factors Bioconductor version: 3.10 Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend…

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Machine Learning – Acroquest Myanmar Technology

Machine Learning Engineer of Acroquest became 40th place in “Kaggle” worldwide Hiroki Yamamoto, a machine learning engineer of Acroquest Technology Co., Ltd., participated in Kaggle competitions hosted by Google, “Google Landmark Retrieval 2021” and “Google Landmark Recognition 2021,” and achieved a Gold Medal in “Google Landmark Retrieval 2021”. This Gold…

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teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol

GitHub – teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time BACKGROUND…

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Nose hoover lammps manual

Nose hoover lammps manual 科学网—[转载]谈谈分子模拟中的能量最小化,弛豫和平衡态 – 周龙 …NVT run with LAMMPS | Tools and tricks for computational A serious man with a comic face-walrus mustache, had long ago wanted to tear the old girl down and replace her with a gleaming…

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Bioinformatics Pipeline Developer job in Bluntisham, Huntingdonshire, Cambridgeshire

We are currently looking for a Bioinformatics Pipeline Developer to join a leading Biotech company based in the Cambridgeshire area. As the Bioinformatics Pipeline Developer you will be working on early cancer detection technology by supporting software developers and bioinformaticians KEY DUTIES AND RESPONSIBILITIES: Your duties as the Bioinformatics Pipeline…

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Chapter 1 Package name | Bioconductor Package Guidelines for Developers and Reviewers

The package name should match the GitHub repository name and is case-sensitive. A package name should be descriptive and should not already exist as a current package (case-insensitive) in Bioconductor nor CRAN. An easy way to check whether your name is already in use is to check that the following…

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What files (fasta, GTF) do I need for RNA seq analysis

What files (fasta, GTF) do I need for RNA seq analysis 1 I am very new to programming in general, and I’m trying my best to teach myself R for analyzing RNA-seq data we have. I am using this guide and have gotten to the step where I need to…

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Development Scientist – Bioinformatics job with New England Biolabs

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 infrastructure,…

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LTF8 – htsjdk 2.0.1 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.0.1 javadoc.io/doc/com.github.samtools/htsjdk/2.0.1 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.0.1/package-list Read more here: Source link

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CrayLabs/smartsim-lammps: Examples of running LAMMPS with SmartSim

LAMMPS is a popular Molecular Dyanmics (MD) library written in C++. This repository integrates the SmartRedis C++ client into a fork (hopefully soon to be merged) of LAMMPS for online data analysis and visualization. An example of the interactive LAMMPS visualization with ipyvolume: Example: Lennard-Jones Melt Benchmark The melt/ directory…

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Answer: Applying Machine Learning on vcf file

Hi, I just wanted to introduce you to one of my packages called `fuc` ([GitHub](https://github.com/sbslee/fuc)). It has a submodule called `pyvcf` ([API](https://sbslee-fuc.readthedocs.io/en/latest/api.html#module-fuc.api.pyvcf)) which is designed for working with VCF files. It implements `pyvcf.VcfFrame` which stores VCF data as `pandas.DataFrame` to allow fast computation and easy manipulation. One of my main…

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gmx_wallcycle.h | searchcode

gmx_wallcycle.h | searchcode PageRenderTime 23ms CodeModel.GetById 14ms app.highlight 6ms RepoModel.GetById 1ms app.codeStats 0ms /pdalcin-Gromacs-GA-458371f/gromacs-4.0.7/include/gmx_wallcycle.h github.com/pdalcin/Gromacs_GA C++ Header…

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Reduced Metagenome Sequencing for strain-resolution taxonomic profiles

Scientists seeking to understand the difference between a healthy and unhealthy gut microbiome often turn to sequencing microbial DNA. Two main approaches are currently used: metabarcoding, also known as targeted amplicon sequencing, and shotgun sequencing of random fragments. While metabarcoding has limited resolution, full shotgun sequencing has improved resolution but…

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NES using DESEQ2 – githubmemory

Hi, I was just wondering could you help with a query I have. I was following your vignette for bulk RNA-seq TF analysis and when I reached the part involving NES I wasn’t sure which column to use from my data. In the vignette you use the t column, coming…

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Version from bioconductor incompatible with R 3.2.2 version

After I run instructions from BioConductor to install the RTCGAToolbox package ## try http if https is not available source(“https://bioconductor.org/biocLite.R”) biocLite(“RTCGAToolbox” I received such an error Warning messages: 1: package ‘RTCGAToolbox’ is not available (for R version 3.2.2) 2: running command ‘”D:/R-32~1.2/bin/x64/R” CMD INSTALL -l “C:UsersMarcinDocumentsRwin-library3.2” C:UsersMarcinAppDataLocalTempRtmp2vpM0w/downloaded_packages/rgl_0.95.1337.tar.gz’ had status 1…

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dabble-of-devops-bioanalyze/bioanalyze-docker-images: Docker Images for Jupyterhub + Bioinformatics

BioAnalyze Docker Images These docker images are built to use as a part of a full stack Bioinformatics Analysis Environment. Each image can be used on it’s own or as a part of a Jupyterhub Cluster. Each image is meant to be a full fledged ecosystem for Bioinformatics. Images: Bioinformatics…

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450k Illumina error for some probe converting hg19 to hg38

450k Illumina error for some probe converting hg19 to hg38 0 Using liftOver to convert CpG probes of 450K Illumina, hg19 to hg38 but some probes can not be converted. Some examples cg23887839 chr1 12606996 12606997 cg24299149 chr1 13501140 13501141 cg07784526 chr1 120838320 120838321 cg18948743 chr1 120838323 120838324 But I…

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bedtools.rb | searchcode

bedtools.rb | searchcode PageRenderTime 19ms CodeModel.GetById 16ms app.highlight 1ms RepoModel.GetById 1ms app.codeStats 0ms /Library/Formula/bedtools.rb github.com/clouded-eas/homebrew Ruby |…

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Codebase of deep learning models for inferring stability of mRNA molecules

Codebase of deep learning models for inferring stability of mRNA molecules, corresponding to the Kaggle Open Vaccine Challenge and accompanying manuscript “Predictive models of RNA degradation through dual crowdsourcing”, Wayment-Steele et al (2021) (full citation when available). Models contained here are: “Nullrecurrent”: A reconstruction of winning solution by Jiayang Gao….

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Feat/support passing index files – githubmemory

v1.10 brought about the new -X option (-X include customized index file), to samtools. github.com/samtools/samtools/pull/978 Is it possible to request for tabix/bcftools/etc? Use case would be for passing in signed s3 urls into all of the various tools. e.g. tabix <signed_vcf_url> -X <signed_vcf_tbi_url> chr2 bcftools view <signed_vcf_url> -X <signed_vcf_tbi_url> chr2…

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Gmod E2 Portal – LoginWave

If you are looking for gmod e2 portal, simply check out our links below : steamcommunity.com/sharedfiles/filedetails/?id=571740596Store Page. Garry’s Mod … portal gun expression 2 (e2). Description … it’s a portal gun, right click or left click with a gravity gun to use it, reload to remove portals steamcommunity.com/sharedfiles/filedetails/?id=70749011 Steam Community:…

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SortingCollection.Codec – htsjdk 1.139 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.139 javadoc.io/doc/com.github.samtools/htsjdk/1.139 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.139/package-list Read more here: Source link

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Ipsedo/LANLEarthquakePrediction: Kaggle challenge LANL Earthquake Prediction

GitHub – Ipsedo/LANLEarthquakePrediction: Kaggle challenge LANL Earthquake Prediction Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time About Kaggle challenge LANL Earthquake Prediction Topics Resources You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh…

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How to get FASTQ reads from the Short Read Archive (SRA)

Getting data out of the short read archive is a tedious and error prone process, thanks to the clunky interfaces and changing methodologies. if you want a subset of the reads say 1000 reads use fastq-dump -X 1000 SRR14575325 if you want the entire file use fasterq-dump SRR14575325 if you…

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post-link.sh | searchcode

post-link.sh | searchcode PageRenderTime 15ms CodeModel.GetById 8ms app.highlight 4ms RepoModel.GetById 1ms app.codeStats 0ms /recipes/bioconductor-hgu133afrmavecs/post-link.sh github.com/bioconda/bioconda-recipes Shell |…

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Error connecting to external databases through celldex

Error connecting to external databases through celldex 1 @swbarnes2-14086 Last seen 8 hours ago San Diego My organization’s IT policies have tightened up with regard to making external connections, and I’m getting errors like localHub=TRUE library(celldex) mouse_imm_ref <- celldex::ImmGenData() Error in value[[3L]](cond) : failed to connect reason: SSL certificate problem:…

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id conversion & the problem of package “org.Hs.eg.db”

clusterprofiler: id conversion & the problem of package “org.Hs.eg.db” 0 I want to implement id conversion using clusterProfiler. But I met a bug as following: I successfully library package org.Hs.eg.db, but I couldn’t load it to implement ID conversion using function bitr in R package clusterProfiler. What’s wrong with it?…

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Dhinagaran-s/Kaggle-Competitions-1 – githubmemory

Description about repository: • This repository consists of all the competitions that I have taken part on Kaggle.• Datasets are provided in each of the folders above, and also the solution to the problem statements have been provided.• Kaggle Profile: www.kaggle.com/anujvyas Competition(s) with ranks: • Titanic: Machine Learning from Disaster…

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The Biostar Herald for Wednesday, October 13, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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GOChord plot problem when using the chor_dat function to create a matrix

GOChord plot problem when using the chor_dat function to create a matrix 0 Hello All, I am trying to create a GOChord plot for circular visualization of the results of gene- annotation enrichment analysis. I created all the data frames myself and cross-checked the types of every column in each…

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How to Ace Data Science Interview by Working on Portfolio Projects

By Abid Ali Awan, Certified Data Scientist. Image by Author. Recruiters nowadays are checking your online presence before contacting you about an interview. They will look for your LinkedIn profile, GitHub, and Kaggle to figure out what value you will bring to their company. The hiring manager will also look for…

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SamReader.Indexing – htsjdk 2.1.1 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.1.1 javadoc.io/doc/com.github.samtools/htsjdk/2.1.1 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.1.1/package-list Read more here: Source link

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meta.yaml | searchcode

meta.yaml | searchcode PageRenderTime 11ms CodeModel.GetById 2ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml github.com/bioconda/bioconda-recipes YAML |…

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Bioconductor/BiocParallel source: R/bpinit.R

.bpinit <- function(manager, FUN, BPPARAM, BPREDO = list(), …) { ## Conditions for starting a cluster, or falling back to (and ## starting) a SerialParam nworkers <- bpnworkers(BPPARAM) # cache in case this requires a netowrk call fallback_condition <- !inherits(BPPARAM, “SerialParam”) && nworkers == 0L || # e.g., in dynamic…

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Bioconductor – esATAC

DOI: 10.18129/B9.bioc.esATAC     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…

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Bioinformatics Manager – Precision Biomarker Labs at Cedars-Sinai

Requisition # HRC0707785 Join us in releasing the power of precise proteomics! The Bioinformatics Manager manages and provides leadership for the overall achievement of bioinformatics and software pipelines for production quality across Precision Biomarker Laboratories (PBL), Dr. Van Eyk’s ACBRI lab, and the Cedars-Sinai Medical…

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dna seq analysis – Banya

Dna Sequencing Data Analysis Simple Software Tools . Omicscript Pipeline For Dna Seq Data Analysis Array Suite Wiki . Dna Sequencing Data Analysis Simple Software Tools . Omicscript Pipeline For Dna Seq Data Analysis Array Suite Wiki . Dna Sequence Alignment Dna Contig Assembly Software Sequence . Dna Sequence Alignment…

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GitHub – matteoeghirotta/lammps-30Oct19

GitHub – matteoeghirotta/lammps-30Oct19 Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time About No description, website, or topics provided. Resources License You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed…

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sam2tsv listing incorrect reference sequence & positions

Duplicate of: github.com/lindenb/jvarkit/issues/190 Hi can anyone help me resolve the issue I’m having with sam2tsv. It is a nifty piece of software but I have been encountering issues with it regarding the numbering of nucleotides it shows for the reference sequence. Here’s what sam2tsv tells me: The nucleotide string marked…

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RRBS methylation analysis

Hello, I want to use HMST-Seq anayzer (www.sciencedirect.com/science/article/pii/S2001037020304232) tool for my RRBS data analysis (directional) but I am stuck at the first step. In order to run HMST-Seq analyzer pipeline, I need CpG.txt or CpG.bed file as an input. So, I first performed bismark analysis on my control and mutated…

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NGSeq/DHPGIndex: This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

General This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes. The pipeline can be deployed in cloud computing environment or in dedicated computing cluster. The tool extends the CHIC aligner gitlab.com/dvalenzu/CHIC with distributed and scalable features. DHPGIndex have been tested…

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Kaggle_airbus_ship_detection – Open Source Agenda

Kaggle Airbus Ship Detection Challenge : 21st solution This project is for Kaggle competiton Airbus Ship Detection Challenge. It can help you quickly get a baseline solution, which is not bad. Related article These guides are only in Chinese: Kaggle新手银牌(21st):Airbus Ship Detection 卫星图像分割检测 用Mask R-CNN训练自己的COCO数据集(Detectron) 辅助操作指南:Docker使用、镜像制作、Demo运行… File strcture airbus ├─0_rle_to_coco…

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October 2021 Galactic News – Galaxy Community Hub

Hello all, October brings Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of trainings, talksm and a Galaxy Papercuts CoFest day too. It also brings news of new job openings on two continents, two new platforms, blog posts (where My Little Pony makes an appearance, really), GTN updates…

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Bioconductor – JctSeqData

DOI: 10.18129/B9.bioc.JctSeqData     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see JctSeqData. Example Junction Count data for use with JunctionSeq Bioconductor version: 3.9 Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data…

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The 2nd place solution of 2021 google landmark retrieval on kaggle.

The 2nd place solution of 2021 google landmark retrieval on kaggle. Environment We use cuda 11.1/python 3.7/torch 1.9.1/torchvision 0.8.1 for training and testing. Download imagenet pretrained model ResNeXt101ibn and SEResNet101ibn from IBN-Net. ResNest101 and ResNeSt269 can be found in ResNest. Prepare data Download GLDv2 full version from the official site….

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marco-mariotti/tiedpyranges: Extends the pyranges module with operations on joined genomic intervals (e.g. exons of same transcript)

GitHub – marco-mariotti/tiedpyranges: Extends the pyranges module with operations on joined genomic intervals (e.g. exons of same transcript) Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time Extends the pyranges module with operations on joined genomic intervals (e.g. exons of same transcript) Install with:…

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Job vacancy in Global Worldwide: Bioinformatics Scientist – Senior Scientist at Arcus Biosciences

Job details Job type full-time Full job description Bioinformatics scientist – senior bioinformatics scientist Arcus is seeking a scientist-srScientist that will work in a highly embedded, collaborative model with colleagues across the organizationCandidate will work closely with translational and biology research scientists in the development of novel therapeutics and biomarkers…

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SherylPhilip/Course-3—Data-Manipulation: This repository contains one of the pre-requisite notebooks for my internship as a Data Analyst at Technocolabs. It includes some of the micro-courses from Kaggle.

GitHub – SherylPhilip/Course-3—Data-Manipulation: This repository contains one of the pre-requisite notebooks for my internship as a Data Analyst at Technocolabs. It includes some of the micro-courses from Kaggle. Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time Techncolabs_Internship_Prequisites (Data-Manipulation) This repository contains one of…

Continue Reading SherylPhilip/Course-3—Data-Manipulation: This repository contains one of the pre-requisite notebooks for my internship as a Data Analyst at Technocolabs. It includes some of the micro-courses from Kaggle.

mdozmorov/excluderanges: Genomic coordinates of problematic genomic regions as GRanges

Genomic ranges of problematic genomic regions that should be avoided when working with genomic data. For human, mouse, and selected model organisms. TL;DR – For human hg38 genome assembly, Anshul recommends ENCFF356LFX exclusion list regions. BED files of exclusion regions are available on the ENCODE project website (Amemiya, Kundaje, and…

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How to get a list of all KEGG ko terms vs names?

How to get a list of all KEGG ko terms vs names? 2 I want to map a list of KEGG terms with their corresponding names. Is it possible to get a list of all KEGG terms and their descriptions/names? kegg annotation rna-seq • 1.0k views Hi. I am not…

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Gene Ontology Bubble Plot using ggplot2

So with your data that seems to look something like this: structure(list(GO_term = structure(c(2L, 4L, 3L, 1L), .Label = c(“Kinase”, “Metabolism”, “Nucleus”, “Photosynthesis”), class = “factor”), Number = c(5L, 10L, 15L, 16L), Class = structure(c(3L, 2L, 1L, 1L), .Label = c(“hs”, “hzs”, “start_duf”), class = “factor”), Type = structure(c(1L, 1L,…

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Bioconductor – ewceData (development version)

DOI: 10.18129/B9.bioc.ewceData     This is the development version of ewceData; for the stable release version, see ewceData. The ewceData package provides reference data required for ewce Bioconductor version: Development (3.14) This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell…

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A Tool for Rapid Sequence Comparison

MinHash Sketch is a method of rapidly comparing large strings or sets. In genomics, you can use it like this: 1) Gather all the kmers in a genome. 2) Apply a hash function to them. 3) Keep the 10000 smallest hashcodes and call this set a “sketch”. If you do…

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fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.

Tool:fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs. 0 fastp, the widely used ultra-fast FASTQ preprocessing and QC tool, and till now has been cited over 2,000 times. Today, a new version, v0.23.0 has been released, with great improvement on performance. The threading and I/O modules have been…

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Bioconductor – LRcellTypeMarkers (development version)

DOI: 10.18129/B9.bioc.LRcellTypeMarkers     This is the development version of LRcellTypeMarkers; for the stable release version, see LRcellTypeMarkers. Marker gene information for LRcell R Bioconductor package Bioconductor version: Development (3.14) This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset…

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Barostat cp2k error

Barostat cp2k error 08-10-2021 right! like your idea. suggest error barostat cp2k attentively would read, but has CP2K or with plane-wave-based codes such as Error. Espresso. In doing so, the Rahman barostat The statistical…

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DeepMind Introduces ‘Enformer’, A Deep Learning Architecture For Predicting Gene Expression From DNA Sequence

Source: deepmind.com/blog/article/enformer DNA contains the genetic information that influences everything from eye color to illness and disorder susceptibility. Genes, which are around 20,000 pieces of DNA in the human body, perform various vital tasks in our cells. Despite this, these genes comprise up less than 2% of the genome. The…

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Software | OCRA Web Portal

SOFTWARE DEVELOPED BY THE BFG All of our work has led at various points to generation of new algorithms and software. In order to ensure that our bioinformatics analyses are reproducible and available to fellow researchers, we have adopted a philosophy of open source and work with public software repositories…

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scatterHatch: an R/Bioconductor package for colorblind accessible visualization of single-cell data

Abstract Summary: Color is often used as a primary differentiating factor in visualization of single-cell and multi-omics analyses. However, color-based visualizations are extremely limiting and require additional considerations to account for the wide range of color perceptions in the population. The scatterHatch package provides software for accessible single-cell visualizations that…

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Single Cell RNA seq imputation with MAGIC

Single Cell RNA seq imputation with MAGIC – scale of output? 1 Hello, I ran MAGIC on some single cell seq data and am curious of the scale of the output? I first used Seurat’s normalization function which converts the raw counts to CPM and then natural log transforms the…

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Scars gmod error fix

Scars gmod error fix 07-10-2021 agree agree, fix error scars gmod something is. will know, many thanks for Vehicle addon for GMod. Contribute to sakarias88/scars-slim development by creating an account on GitHub. SCars Slim….

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Installing Picard

Installing Picard 1 Hi, I’m trying to install Picard on my Ubuntu, I can’t understand the install process because I’m not familiar with java. It seems there are two ways to install Picard. One is using git clone and the other is zip file. zip file link – broadinstitute.github.io/picard/ github…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

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SonwYang – Github Help

snow’s Projects awesome-image-classification A curated list of deep learning image classification papers and codes awesome-knowledge-distillation Awesome Knowledge Distillation building-extraction CenterUnet CenterUnet: Unet version of CenterNet Objects As Points with mask branch. Change-Detection-Review A review of change detection methods, including codes and open data sets for deep learning. From paper: change…

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interesting kaggle datasets

Kaggle ARC challenge has set May 27 as the final submission deadline for the ARC challenge. Kaggle Datasets. The internet is a treasure trove of valuable information for aspiring data scientists. • updated 2 years ago (Version 3) Data Tasks Code (1,473) Discussion (1) Activity Metadata. (Some might need you…

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Bioconductor Case Studies Use R

Bioconductor Case Studies Use R Analysing time course microarray data using Bioconductor MeV+R: using MeV as a graphical user interface for Omic association studies with R and Bioconductor (eBook Results: We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles…

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The Jackson Laboratory hiring Postdoctoral Associate | Bioinformatics in Farmington, Connecticut, United States

The Robinson Lab at The Jackson Laboratory for Genomic Medicine (JAX-GM) is seeking a full-time Postdoctoral Associate for bioinformatics software and web development. The Robinson Lab’s team of expert biological curators, bioinformaticians, and computer scientists maintain and enhance a knowledge extraction and refinement process that delivers an essential set of…

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CryoSky – Github Help

Cryosky’s Projects AlloType Methods to predict allosteric regulation type. alphafold Open source code for AlphaFold. alphafold-1 Install alphafold on the local machine, get out of docker. AlphaFold_oligomer The repository for modeling of oligomeric protein structure using AlphaFold. alphafold_pytorch An implementation of the DeepMind’s AlphaFold based on PyTorch for research awsemmd…

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

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nlp – What is the algorithm behind pairwise2 align in BioPython?

The package BioPython allows to compute pairwise local or global alignement, through different functions (align.globalxx, align.localxx, …). However, I have not found anywhere the algorithm on which this alignement is based. The code (source, doc) states: “Pairwise sequence alignment using a dynamic programming algorithm”, and that is all. Is there…

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Bioconductor – rGREAT

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see rGREAT. Client for GREAT Analysis Bioconductor version: 3.2 This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user’s input and automatically retrieving…

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Bioconductor – DMRScan

DOI: 10.18129/B9.bioc.DMRScan     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DMRScan. Detection of Differentially Methylated Regions Bioconductor version: 3.10 This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The…

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Frequency of the gene expression in Seurat

DotPlot computes the fraction of cells expressing a gene in each group (metadata column), so you can cheat a little and extract the results from it [source]. library(“Seurat”) features <- c(“PECAM1”, “CD14”) group_column <- “clusters” perc_exp <- DotPlot(seu, features=features, group.by=group_column)$data[, c(“features.plot”, “id”, “pct.exp”)] The returned data will look something like…

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Biocmanager Install Vs Install Packages

Introduction to RNAseq I Day 3 Nicolas Rochette (EEB/ISG, UCLA) Karolina Kaczor-Urbanowicz (Oral Biology & Medicine, UCLA) UCLA Institute for Quantitative and Computational BiologyOver-representation (or enrichment) analysis is a statistical method that determines whether genes from pre-defined sets (ex: those beloging to a specific GO term or KEGG pathway) are…

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ChIP-seq Peak calling from BED or WIG file

ChIP-seq Peak calling from BED or WIG file 1 Peak callers such as macs can use BED files that contain read coordinates to return peak lists. Something basically like: github.com/macs3-project/MACS macs2 callpeak -t that_bed_file.bed -f BED Login before adding your answer. Traffic: 2658 users visited in the last hour Read…

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The Biostar Herald for Tuesday, October 05, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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How To Extract A Sequence From A Big (6Gb) Multifasta File ?

How To Extract A Sequence From A Big (6Gb) Multifasta File ? 11 I want to extract some sequences using ID from a multifasta file. Using perl is not possible because it gave an error when indexing the database. Maybe because of it’s size? Is there any way to this…

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Bioconductor – MADSEQ

DOI: 10.18129/B9.bioc.MADSEQ     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MADSEQ. Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data Bioconductor version: 3.10 The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the…

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Bioconductor – Heatplus

DOI: 10.18129/B9.bioc.Heatplus     Heatmaps with row and/or column covariates and colored clusters Bioconductor version: Release (3.6) Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is…

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Postdoctoral Fellow – Translational Research in Diabetes – Bioinformatics and Computational Science

Job Description About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6,000 employees, is dedicated to the prevention and cure of cancer, type 1 diabetes, type 2 diabetes and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. City of Hope…

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Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)

Hi all, I am a PhD student with biology background. I recently inherit a RNA Sequencing project from another PhD student in my lab. We already have paired-ended RNA-Seq data generated from Illumina HiSeq but haven’t started analysis yet. I have basic Linux command line training but have no idea about how…

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how to get secondary structure from DSSP?

Here is Biopython’s DSSP code, with typical use shown near the top. It is not difficult to extract this information on your own by reading contents of column 17 of the DSSP output, following this line: # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H–>O O–>H-N N-H–>O O–>H-N TCO KAPPA ALPHA…

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