Tag: RSQLite

Deleting a column from data frame and then running DESeq2

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

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R packages: Missing “suggests” dependency during installation. – General

Hi folks! I’ve encountered an intriguing issue while conducting a package installation process. Currently, I’m working on R version 4.2.1 within the Posit Workbench 2023.03.1+446.pro1, “Cherry Blossom” environment. I’ve developed a package named APIUtilizeR and subsequently uploaded it to our internal POSIT Package Manager. Within the DESCRIPTION file of this…

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RSQLite & targets in R

I want to create a database for efficient queries, but using with targets. Is there a better alternative to open and close connection? tar_target(database, format = “file”, command = { db_file_name <- Sys.getenv(“DB_PATH”, “database.sqlite”) db <- dbConnect(SQLite(), db_file_name) dta_to_db(db, crsp_daily, “crsp_daily”) dta_to_db(db, crsp_monthly, “crsp_monthly”) dta_to_db(db, analist_coverage, “analist_coverage”) dbwriteTable(db, industry_classification, “industry_classification”)…

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removeBatchEffect with non-linear model fit

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

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ScRNAseq analysis scran :: quickcluster Error

ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…

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Accepted r-cran-rsqlite 2.3.3-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Tue, 21 Nov 2023 21:04:55 +0100 Source: r-cran-rsqlite Architecture: source Version: 2.3.3-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-cran-rsqlite (2.3.3-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: b8701a7d846703ed341b6d9f0da1772ede7b0025 2403 r-cran-rsqlite_2.3.3-1.dsc ce7d7f21085580a6ea1bd9790f621aecd23c170b…

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R ggplot2::reexports — EndMemo

R reexports — ggplot2 These objects are imported from other packages. Follow the links below to see their documentation. grid arrow, unit scales alpha . ggplot2::reexports is located in package ggplot2. Please install and load package ggplot2 before use. install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) ggplot(mpg, aes(displ, hwy)) + geom_point(alpha = 0.5,…

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R RSQLite::reexports — EndMemo

R reexports — RSQLite These objects are imported from other packages. Follow the links below to see their documentation. DBI Id . RSQLite::reexports is located in package RSQLite. Please install and load package RSQLite before use. Same Names: ggplot2::reexports, devtools::reexports, tibble::reexports, tidyselect::reexports, purrr::reexports, tidyr::reexports, callr::reexports, testthat::reexports, broom::reexports, sf::reexports, lubridate::reexports, openssl::reexports,…

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Function Repository Quiz 1 NO GGPLOT .pdf – Function Repository 14 September 2022 01:08 PM Data Reading read csv /filename skip = value Reads

Data Reading read_csv(“/filename”, skip = value)Reads default csv’s and skips the value number of rows. Library(readr) read_tsv(“/filename”, skip = value)Reads default tab seperated sheets and skips value number of rows. Library(readr) read_delim(“/filename”,delim = “delimiter”, col_names = FALSE)General reading function, specifying the delimiter, saying we have no column names to assign…

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Bioconductor – AnnotationHub

DOI: 10.18129/B9.bioc.AnnotationHub     Client to access AnnotationHub resources Bioconductor version: Release (3.6) This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be…

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SparseArray unable to install on Bioc 3.18

SparseArray unable to install on Bioc 3.18 0 @f33be25c Last seen 6 hours ago United States I have been using DESeq2 now for several months and my code has been working just fine for my analysis. However today I was unable to load the DESeq package. It appears the issue…

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R: Class SQLiteResult (and methods)

R: Class SQLiteResult (and methods) SQLiteResult-class {RSQLite} R Documentation Class SQLiteResult (and methods) Description SQLiteDriver objects are created by dbSendQuery() or dbSendStatement(), and encapsulate the result of an SQL statement (either SELECT or not). They are a superclass of the DBIResult class. The “Usage” section lists the class methods overridden…

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Bioconductor – EpiTxDb

DOI: 10.18129/B9.bioc.EpiTxDb   Storing and accessing epitranscriptomic information using the AnnotationDbi interface Bioconductor version: Release (3.18) EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA…

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couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

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How To Install r-cran-rsqlite on Ubuntu 22.04

In this tutorial we learn how to install r-cran-rsqlite on Ubuntu 22.04. r-cran-rsqlite is Database Interface R driver for SQLite Introduction In this tutorial we learn how to install r-cran-rsqlite on Ubuntu 22.04. What is r-cran-rsqlite r-cran-rsqlite is: This package embeds the SQLite database engine in R and provides an…

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Annotation hub and clusterProfiler errors

Annotation hub and clusterProfiler errors 1 @33343537 Last seen 4 hours ago Norway How can I get AnnotationHub() run? Also, clusterProfiler is not working because I am unable to install HPO.db > ah <- AnnotationHub() **Error in `collect()`: ! Failed to collect lazy table. Caused by error in `db_collect()` >…

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R: SQLite transaction management

R: SQLite transaction management sqlite-transaction {RSQLite} R Documentation SQLite transaction management Description By default, SQLite is in auto-commit mode. dbBegin() starts a SQLite transaction and turns auto-commit off. dbCommit() and dbRollback() commit and rollback the transaction, respectively and turn auto-commit on. DBI::dbWithTransaction() is a convenient wrapper that makes sure that…

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Working with databases and SQL in RStudio

In today’s data-driven world, the interface between SQL (Structured Query Language) and R has become a must-have for data professionals. SQL empowers us to efficiently interact with relational databases, while R programming language is versatile for data analysis. Combining these two powerful tools can dramatically increase your data conversion capabilities….

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Bioconductor – pd.feinberg.mm8.me.hx1 (development version)

DOI:10.18129/B9.bioc.pd.feinberg.mm8.me.hx1 This is thedevelopmentversion of pd.feinberg.mm8.me.hx1; for the stable release version, seepd.feinberg.mm8.me.hx1. Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Bioconductor version: Development (3.17) Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Author: Martin Aryee Maintainer: Martin Aryee Citation (from within R, entercitation(“pd.feinberg.mm8.me.hx1″)): Installation To install this package, start R (version “4.3”) and enter:…

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R RSQLite::dbWriteTable — EndMemo

R dbWriteTable — RSQLite Functions for writing data frames or delimiter-separated files to database tables. RSQLite::dbWriteTable is located in package RSQLite. Please install and load package RSQLite before use. ## S4 method for signature ‘SQLiteConnection,character,data.frame’ dbWriteTable( conn, name, value, …, row.names = pkgconfig::get_config(“RSQLite::row.names.table”, FALSE), overwrite = FALSE, append = FALSE,…

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DeSeq2 data comparison and extracting outputs

Hi, I have an RNA-seq experiment where there are 2 conditions and 2 genotypes. I am trying to figure out how to output the 2 conditions with 2 genotypes from the dds object. I have read online resources, however, it is still not clear what is extracted. I followed and…

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r – RStudio repeatedly crashes/freezes and weird dplyr errors at random points in code

I’m running code in an R project after updating to newer versions of R/RStudio and the most recent tidyverse package versions. When I run certain dplyr/tidyverse functions, primarily joins, pivoting, or summarizing, I either have R crash, freeze, or get strange errors. For example, when I tried to summarize across…

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How To Import A Data Set Into R

Source: Rstudio.com Are you a data analyst or a data scientist looking to import a dataset into R for analysis? Look no further! In this article, we will guide you through the process of importing a data set into R, step by step. R is a powerful programming language and…

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TCGAbiolinks not working anymore

TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…

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Bioconductor – biodb

DOI: 10.18129/B9.bioc.biodb   biodb, a library and a development framework for connecting to chemical and biological databases Bioconductor version: Release (3.17) The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, …), as well as to in-house local database files (CSV, SQLite), with easy retrieval…

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CRAN Package Check Results for Package RSQLite

CRAN Package Check Results for Package RSQLite Last updated on 2023-09-07 11:53:17 CEST. Flavor Version Tinstall Tcheck Ttotal Status Flags r-devel-linux-x86_64-debian-clang 2.3.1 185.54 83.95 269.49 OK r-devel-linux-x86_64-debian-gcc 2.3.1 160.89 71.75 232.64 OK r-devel-linux-x86_64-fedora-clang 2.3.1 347.65 OK r-devel-linux-x86_64-fedora-gcc 2.3.1 434.27 OK r-devel-windows-x86_64 2.3.1 175.00 116.00 291.00 OK r-patched-linux-x86_64 2.3.1 193.84 80.73…

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R studio freezes when monocle3 is installed – RStudio IDE

Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…

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Creating Double The Columns Than There Are Samples: DEXseq

I am trying to use DEXseq and I was told that I could output normalized counts using the following method by my supervisor: library(“DEXSeq”) # Create the DEXSeqDataSet object dxd <- DEXSeqDataSetFromHTSeq( countsFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile ) #Normalize normFactors <- matrix(runif(nrow(dxd)*ncol(dxd),0.5,1.5), ncol=ncol(dxd),nrow=nrow(dxd), dimnames=list(1:nrow(dxd),1:ncol(dxd))) normFactors…

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Problem installing Dependencies for R – JupyterHub

I am trying to set up an R env and install base packages for all users. The package lives on gitlab and I am using the following to install it. What happens is that during the deployment everything works fine and I can see this package being built and end…

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bad_weak_ptr error knitting rmarkdown – R Markdown

Hello, I got an error upon knitting, that can only be removed by removing all caches and re knitting. However, I am not sure how to reproduce this bug, so I have not included a self-contained and reproducible example. The code is only to plot a ggplot object. The error…

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Bioconductor – pd.rae230a (development version)

DOI: 10.18129/B9.bioc.pd.rae230a   This is the development version of pd.rae230a; for the stable release version, see pd.rae230a. Platform Design Info for The Manufacturer’s Name RAE230A Bioconductor version: Development (3.18) Platform Design Info for The Manufacturer’s Name RAE230A Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

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Quarto render error with chinese docs and knitr opts_chunk set in YAML heading – #2 by goo – RStudio IDE

A minimal demo: — title: “demo” lang: zh knitr: opts_chunk: collapse: false format: gfm: default — 第一行 第二行 – 第三行 – 第四行 – 第五行 The output # demo 第一行二行 第三行 第四行 第五行 However, the expected output is # demo 第一行 第二行 – 第三行 – 第四行 – 第五行 There are more…

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IsoformSwitchAnalyzeR Error in reading GTF file

IsoformSwitchAnalyzeR Error in reading GTF file 0 Hi, I am using IsoformSwitchAnalyzeR v1.21.0 in R 4.3.0 environment using RStudio (2023.06.0+421 “Mountain Hydrangea” Release). When I try to import GTF file (obtained from Ensembl Plants) I get the following error ; Step 1 of 7: Checking data… Step 2 of 7:…

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VariantFiltering error

VariantFiltering error 0 @andrew-beggs-5579 Last seen 15 hours ago United Kingdom Hi Trying to run VariantFilter, manage to import fine, PED file is pretty standard: FAM001 SAMPLE_C SAMPLE_P1 SAMPLE_P2 1 2 FAM001 SAMPLE_P1 0 0 0 1 FAM001 SAMPLE_P2 0 0 0 1 > vfpar VariantFiltering parameter object VCF file(s):…

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DESeq2 with nbinomGLM issues

DESeq2 with nbinomGLM issues 0 @andrebolerbarros-16788 Last seen 6 hours ago Portugal Hi everyone, I was performing some DEGs and got this message: Warning messages: 1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, … : the line search routine failed, possibly due to insufficient…

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sql – Safety of transactions with RSQLite and pool

Is the following safe to use in a Shiny app (that might have a few concurrent users): dbExecute(pool, “BEGIN TRANSACTION;”) dbExecute(pool, “INSERT INTO cars (speed, dist) VALUES (1, 1);”) dbExecute(pool, “INSERT INTO cars (speed, dist) VALUES (3, 3);”) dbExecute(pool, “COMMIT TRANSACTION;”) It does not seem to cause any issues but…

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bioconductor caches fails to load/corrupted for annotation databases

bioconductor caches fails to load/corrupted for annotation databases 0 I’m unable to load annotation databases such as transcription databases due to corrupt caches. The problem still persists after reinstalling packages I tried following leads in this biconductor post but doesn’t solve the problem. Any suggestions would be gladly appreciated. Thanks…

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Administration Guide – R Package Dependencies

The following is a list of all of the R packages RStudio depends on in some way. None of these packages are necessary for the basic operation of RStudio; they all enable additional IDE functionality as noted in in Features. This information is also available in the IDE itself using…

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r – Support of nanotime by RSQLite

I am looking into what is required to support nanotime objects in RSQLite queries. They are just integer64 wrappers. Here is an example: con <- DBI::dbConnect(RSQLite::SQLite(), “:memory:”) ts <- nanotime::as.nanotime(Sys.time()) str(ts) # integer64 2023-06-04 17:30:21.669581000 DBI::dbGetQuery(con, ‘SELECT :ts AS x’, list(‘ts’ = ts)) # returns 5.757609e-196 tsi <- bit64::as.integer64(ts) DBI::dbGetQuery(con,…

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lfcshrink error DESeq2

Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…

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Bioconductor – MsBackendSql

DOI: 10.18129/B9.bioc.MsBackendSql   SQL-based Mass Spectrometry Data Backend Bioconductor version: Release (3.17) SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint,…

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C R Package Dependencies | RStudio Server Professional Edition 1.3.937-3

base64enc 0.1-3 R Markdown crayon 1.3.4 Plumber R APIs, Shiny curl 4.2 Publishing DBI 0.8 Database Interface, RSQLite devtools 1.11.1 R Unit Testing digest 0.6 R Markdown, Shiny evaluate 0.13 R Markdown glue 1.3.0 R Markdown haven 0.2.0 SPSS/SAS/Stata Import highr 0.3 R Markdown htmltools 0.3.6 R2D3, R Markdown, Shiny,…

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Bioconductor – pd.2006.07.18.mm8.refseq.promoter

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see pd.2006.07.18.mm8.refseq.promoter. Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter Bioconductor version: 2.11 Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter Author: Martin Aryee Maintainer: Martin Aryee <aryee at jhu.edu> Citation (from within R, enter citation(“pd.2006.07.18.mm8.refseq.promoter”)): Installation To…

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Bioconductor – synaptome.db (development version)

DOI: 10.18129/B9.bioc.synaptome.db   This is the development version of synaptome.db; for the stable release version, see synaptome.db. Synamptosome Proteome Database Bioconductor version: Development (3.17) The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse…

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Gene duplicate

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

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Error generating counts df for use with DRIMSeq/DEXseq

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

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TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

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merge (all=T) error – rstudio

I have two installations of RStudio with each different updates of the packages. On the recent packages I get two errors that I don’t have with the previous packages. Can someone tell me what the problem is? Error 1: df_lofreq_3_DEL <- merge(df_lofreq_3_DEL, deletions_VAR_df_sub_freq, by.x=”VAR_MUT”, by.y=”lofreq_del”, all=T) Error in if (all.x)…

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DESeq2: invalid class “GRangesList” object

Hi all, I am not sure if this is the right place to ask this question, but I’ve just updated my DESeq2 package from version 1.4.5 to version 1.6.3 and my scripts are no longer working. Specifically, I get the following error when generating a DESeqDataSet object with the function…

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[bullseye] r-cran-ggplot2 depends on missing libpq5 v13.8

Hi, I am on bullseye and am trying to install the package r-cran-ggplot2. This fails with E: Failed to fetch deb.debian.org/debian/pool/main/p/postgresql-13/libpq5_13.8-0%2bdeb11u1_amd64.deb 404 Not Found [IP: 146.75.122.132 80] (full output below). There seems to be a dependency on libpq5 version 13.8 whereas the version available for bullseye is 13.9. Any ideas how to…

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Bioconductor – ChemmineR

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see ChemmineR. Cheminformatics Toolkit for R Bioconductor version: 2.13 ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of…

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HTSeqGenie run error

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

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Potential problem with independent filtering in DESeq2

Potential problem with independent filtering in DESeq2 1 @8a6e6497 Last seen 16 hours ago United States Hello, I was routinely using DESeq2 for some small RNA-seq datasets, and suddenly I noticed that FDR corrections are too aggressive. After some investigation, I found out that independent filtering is wrongly determining the…

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RSQLite package – RDocumentation

Embeds the SQLite database engine in R, providing a DBI-compliant interface. SQLite is a public-domain, single-user, very light-weight database engine that implements a decent subset of the SQL 92 standard, including the core table creation, updating, insertion, and selection operations, plus transaction management. You can install the latest released version…

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Strange Cook’s Values with DESeq2

Hi, I’m currently trying to assess fold change when comparing two different sample types using DESeq2 package and I’m getting weird Cook’s distance values which are causing major problems. The two different samples have different amounts of replicates (6 replicates vs 5 replicates) which might be the reason for these…

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Bioconductor – metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

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Unable to install clusterProfiler on Mac M1

Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…

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getTable ignores query ranges

HI everyone. I have a set of mouse SNPs (~974) from GRCm39 that I’m trying to get either GERP or UCSC Conservation scores on. To do this, I’m using rtracklayer to try to query the ranges of the SNP and return the multiz35way conservation score. However, when I do this,…

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microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene

microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene 0 @lluis-revilla-sancho Last seen 8 hours ago European Union I was looking to some examples and I could retrieve the microRNAs of the hg19 transcriptome, but not from the hg38 transcript annotation. I realized this might be because TxDb.Hsapiens.UCSC.hg38.knownGene doesn’t have a miRBase build ID,…

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Error printing a CompressedGRangesList

I’m trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation: GRanges object with 872900 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr10 48196 * [2] chr10 48486 * [3] chr10 49247 * [4] chr10 49258…

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Error in UseMethod(“rescale”)

Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…

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r – Cannot Install maftools into BiocManager due to RSQLite

I am a relatively new R-user. I am currently working on trying to read .maf files via the maftools package released by Bioconductor. I am following the instructions as posted on the Bioconductor website (www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I…

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lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

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Log2FC values slightly higher in some genes after DESeq2 shrinkage

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

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Bioconductor – lumi

DOI: 10.18129/B9.bioc.lumi     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lumi. BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Bioconductor version: 3.12 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina…

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[BioC] rtracklayer 1.6: invalid class “ucscCart” object

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

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Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

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subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

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RSQLite: binding sets and scalars in the same select query

Why do you specify y = I(list(7,6)) instead of y=c(6,7)? This seems to work: dbGetQuery (c, “select * from tst where x = ? and y in (?)”, data.frame(x=1, y=c(7,6))) You might be looking for expand.grid. dbGetQuery (c, “select * from tst where x = ? and y in (?)”,…

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Questions tagged rsqlite – DevDreamz

Python Javascript Linux FAQ LoginSignup PUBLIC All Questions Tags Snippets Jobs rsqlitersqlite rsqlitedata-tablesqliter rsqlitersqlite sqlrdatabasersqlite sqlrprepared-statementrsqlitedatabase rr-markdowndata-wranglingrsqlitesql rrsqlitesqlite rsqliter-dbir rsqlitersqlite sqldfrrsqlite PreviousNext Recent Posts show same id one time but in column count how many times php Assign bundle or argument to ImageView in Android ValueRequiredException during RSS feed parsing…

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Bioconductor installation problems

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01) — “Bird Hippie” Copyright (C)…

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Bioconductor Package Installation

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

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rsqlite database python (1) – Code Examples

python – OperationalError: database is locked I have made some repetitive operations in my application(testing it), and suddenly I’m getting a weird error: OperationalError: database is locked I’ve restarted the server, but the error persists.… how to close resultset in RMySQL? I…

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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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Installation and set up of R6 rocker object

Installation of current released version from CRAN install.packages(“rocker”) Installation of current development version from GitHub install.packages(“devtools”) devtools::install_github(“nikolaus77/rocker”) Create new rocker database handling object Option 1 db <- rocker::newDB() # New database handling object #> dctr | New object Option 2 db <- rocker::rocker$new() # New database handling object #> dctr…

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DESeq2 and high prefiltering cutoff

DESeq2 and high prefiltering cutoff 1 @255004b1 Last seen 3 hours ago United States Hi, I am curious about prefiltering with DESeq2. I understand from this site and reading the DESeq2 vignette that prefiletering is really unnecessary as DESeq2 has a stringent filtering that it does. However, I’m seeing better…

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Mixed Type: option to return list instead of coercing

I now think that the default mode should be to return an error here. That ship has sailed now. SQLite is fairly unique in its flexibility to store arbitrary data in the columns. For your use case I’d recommend segmenting by data type: library(RSQLite) con <- dbConnect(SQLite(), “:memory:”) dbGetQuery(con, “SELECT…

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pmk21/rsqlite – gitmetadata

A simple SQLite clone in Rust. This is basically a translation of the C code present on this brilliant tutorial into Rust(not fully idiomatic). This code contains implementation only upto Part 5 in the tutorial. This a very simple database and is a small project I took up to gain…

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traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

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R connection to sqlite – Stackify

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

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Having problem with RSQLite : RStudio

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

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sqliteCopyDatabase function – RDocumentation

Description Copies a database connection to a file or to another database connection. It can be used to save an in-memory database (created using dbname = “:memory:” or dbname = “file::memory:”) to a file or to create an in-memory database a copy of another database. Usage sqliteCopyDatabase(from, to) Arguments from…

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Accepted r-cran-rsqlite 2.2.9-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Wed, 29 Dec 2021 01:12:39 +0530 Source: r-cran-rsqlite Architecture: source Version: 2.2.9-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-cran-rsqlite (2.2.9-1) unstable; urgency=medium . * Team Upload. [ Andreas Tille ] * Disable…

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How do I “flush” data to my RSQLite disk database?

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

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sqldf : create table from data frame error: “no such table”. and two tables created instead of one

UPDATE: newest versions of RSQLite and sqldf do not have the incompatibility issues addressed by this question i.e.: sqldf_0.4-10 RSQLite_1.1-2 work together well – Nathan All: Thanks to G. Grothendieck for pointers to incompatibility issues introduced by RSQLite 1.1-1. As stated in the comment to the answer, downgrade RSQLite to…

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identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

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r – RSQLite Error “hash is not an exported object”

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

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Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

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r – RSQlite – Find values with most occurences in group

I’m using RSQlite to import Datasets from an SQlite-Database. There are multiple millions of observations within the Database. Therefor I’d like to do as much as possible of Data selection and aggregation within the Database. At some point I need to aggregate a character variable. I want to get the…

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Bioconductor – pd.ht.hg.u133a

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.ht.hg.u133a. Platform Design Info for The Manufacturer’s Name HT_HG-U133A Bioconductor version: 2.14 Platform Design Info for The Manufacturer’s Name HT_HG-U133A Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

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Bioconductor – pd.hg.focus

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.hg.focus. Platform Design Info for The Manufacturer’s Name HG-Focus Bioconductor version: 2.14 Platform Design Info for The Manufacturer’s Name HG-Focus Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

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Bioconductor – pd.raex.1.0.st.v1

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.raex.1.0.st.v1. Platform Design Info for Affymetrix RaEx-1_0-st-v1 Bioconductor version: 2.14 Platform Design Info for Affymetrix RaEx-1_0-st-v1 Author: Benilton Carvalho Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“pd.raex.1.0.st.v1”)): Installation To…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Bioconductor – pd.feinberg.mm8.me.hx1

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see pd.feinberg.mm8.me.hx1. Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Bioconductor version: 2.8 Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Author: Martin Aryee Maintainer: Martin Aryee <aryee at jhu.edu> Citation (from within R, enter citation(“pd.feinberg.mm8.me.hx1”)): Installation To…

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weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

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