Tag: .tar.gz

Efficient Ways To Get Help On An R Package In RStudio

Article Summary Box Familiarize yourself with RStudio’s help system, which is essential for efficient programming. Strategies for accessing detailed documentation for specific R packages directly within RStudio. Leverage RStudio’s advanced search features for streamlining the process of finding relevant help information. Interpreting and utilizing package vignettes and manuals, an often-overlooked…

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Species coverage in the NCBI protein NR database ?

Hi Biostars, I am currently trying to build a Eukaryote version of the NCBI NR database and I am not really sure that I fully understand how the NR is implemented. Here is the code that I’m using to do so : #!/usr/bin/bash ############## # DOWNLOAD FULL NR ############## baseURL=”https://ftp.ncbi.nlm.nih.gov/blast/db/”…

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blastn Error: mdb_env_open: Cannot allocate memory

blastn Error: mdb_env_open: Cannot allocate memory 0 Dear All, I downloaded nt database using wget ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz it has 115 nt files. I run blastn using a genome file to the nt database but I received the error below: Error: mdb_env_open: Cannot allocate memory I tried different versions of blastn (2.9.0,…

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How to Install DataSpell on Linux: A Comprehensive Guide

With the boom of AI and data science, there’s a rise in the need for data scientists and machine learning engineers as well. Those engineers and developers need tools like an IDE to write their code and train models. A specialized IDE can enhance their workflow and improve their efficiency….

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a cross-platform, efficient, practical and pretty CSV/TSV toolkit

Tool:csvtk – a cross-platform, efficient, practical and pretty CSV/TSV toolkit 2 Hi all, I’d like to share my another practical toolkit, csvtk, after introducing SeqKit yesterday. Introduction Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data sicence. People…

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Bioconductor MicroRNAArrayData

Comment: why is downloading the .tar.gz file for a given bioconductor package, then insta by Ndimensional ▴ 20 Sorry about the N=2. That was meant to read 20 (following the 10 in the previous sentence), my apologies there. The provided link to MSMB-… Answer: smallRNA-seq analysis batch correction in limma…

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why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective that BiocManager::install()

# consider the following: LibList=c(‘this’, ‘that’, ‘theother’, … , ‘libraryN – 1’, ‘library N’) LibsToInstall<-LibList[ !(LibList %in% as.data.frame(installed.packages())[[“Package”]]) ] BiocManager::install(LibsToInstall, update=TRUE, ask=FALSE) lapply(TcgaUtilLibs, library, character.only = TRUE) Irrespective of the version of R/Bioconductor, as Liblist grows beyond 10, the probability of an installation can only increase; by the time N=2,…

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Prediction of Ribosomal RNA Genes Using RNAmmer Software

Introduction Ribosomal RNA (rRNA) genes are known to be an integral part of ribosome synthesis machinery hence been studied extensively. Due to their repetitive nature, evolutionary converseness, and ubiquitous distribution /omnipresence, these genes are playing a key role in varying functions and mechanisms including maintenance of genome integrity, control of…

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Importing OpenAPI schema | FortiADC 7.0.1

Importing OpenAPI schema An OpenAPI schema file defines or describes the API including information like the API URL, parameter names in the URL, type of data parameters should have (string, integer, etc), where parameters are submitted (URL, header, body, etc.), and so on. For more information about OpenAPI files, see…

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fasta – adding multiple files in folder and zipping in loop

fasta – adding multiple files in folder and zipping in loop – Bioinformatics Stack Exchange …

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rstudio desktop installation on Ubuntu 23-04 – rstudio

Hello, I’m trying to install Rstudio on my PC with Ubuntu 23.04 (so non LTS). I tried the last .deb or .debian.tar.gz packages from Posit website unsuccesful. The error showed are: R Session Startup Failure Report RStudio Version RStudio 2023.03.0+386 “Cherry Blossom ” (3c53477a, 2023-03-09) for Ubuntu Jammy Mozilla/5.0 (X11;…

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Gromacs Installation Issue – AMD Community

Dear Community,   This is Pim, a new EPYC user. I just DIYed a workstation as following:     – Supermicro H11DSi     – EPYC 7B12 * 2     – Samsung RECC 3200 32G * 16     –  Samsung 980 Pro 2t     – Centos 7…

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No alias or index file found for nucleotide database

BLAST Database error: No alias or index file found for nucleotide database 1 Hi, I have an issue it has been already discuss here a lot, but I cannot find what i’m doing wrong.. For a blastn alignement against the human_genome DB I downloaded the database from the NCBI: wget…

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Importing OpenAPI schema | FortiADC 7.2.0

Importing OpenAPI schema An OpenAPI schema file defines or describes the API including information like the API URL, parameter names in the URL, type of data parameters should have (string, integer, etc), where parameters are submitted (URL, header, body, etc.), and so on. For more information about OpenAPI files, see…

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Bioconductor URI, fallback and time-machine

Hi,On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@gmail.com> wrote: Toggle quote (17 lines) > Currently, the URI scheme (see ‘bioconductor-uri’ in> guix/build-system/r.scm) is:>> bioconductor.org/packages/release/data/<type-url-part>/src/contrib/<upstream-name>-<version&gt;.tar.gz>> which leads to 2 issues:>> 1. when Bioconductor updates their release, some package versions are> updated too, and so, the upstream return 404.> 2. for…

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More than one archive specified. Try –help.

Package: routine-update Version: 0.0.6 Severity: important Hi Andreas, when working on making sure the python-biopython watch file was appropriately fixed, I saw routine-update choke with the following error: $ routine-update gbp:info: Fetching from default remote for each branch gbp:info: Branch ‘master’ is already up to date. gbp:info: Branch ‘pristine-tar’ is already up to date. gbp:info: Branch…

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.tar.gz = same size as before?

BAM compression: .tar.gz = same size as before? 2 I tried to compress 5 bam files using: tar -czvf original_bams.tar.gz *.bam The resulting file sizes (“ll –block-size=M”) are: 8067M file1.bam 6962M file2.bam 10662M file3.bam 7794M file4.bam 7346M file5.bam 40828M original_bams.tar.gz There’s a difference of 3MB between the archive and the…

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