Questions tagged [bioconductor]

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.

Filter by
Sorted by
Tagged with
1 vote
0 answers
30 views

How to tune and use the MetaVolcanoR package

I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
2 votes
0 answers
44 views

How to adjust by multiple variables using ComBat-Seq?

I am trying to adjust my RNA data using ComBat-Seq (from sva R package) since I realised that there are 3 batches that I need ...
  • 121
1 vote
1 answer
43 views

Converting Chip-seq fastq format ({$x_k$} list of seq segments) to genome browser {sequence $x_i$, count-number $y_i$} format

Very new to bioinformatics. I am trying to figure out the steps required to convert a chip-seq fastq file into a genome browser track, with the end goal of being able to access the sequence (x) vs. ...
1 vote
1 answer
64 views

Common tools for generating results and visualizations for bioinformatics and genomics publications

I am a computational scientist with background in computer science and engineering however very new to the field of bioinformatics and computational genomics. Looking at papers in nature, PLOS, Cell, ...
1 vote
1 answer
30 views

Retrieve chromosome number with just RSID?

I have ~500,000 rsids - but want which chromosome each SNP resides on. How can I do this? MarkerName A1 A2 rs2326918 a g rs7929618 c g rs66941928 t c I want ...
  • 111
2 votes
2 answers
62 views

BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code

I am using BiocManager::install("DiffBind") to install the package "DiffBind" on CentOS_7, I got the error: ...
  • 33
2 votes
0 answers
20 views

DeconRNASeq: Extract gene names from returned mixing proportions

This question was also asked on Biostars I am using the Bioconductor package "DeconRNASeq" to perform tissue deconvolution. Let's say I run the following code (this is from the manual): <...
  • 21
2 votes
3 answers
69 views

beginner RNA-seq Replicate papers

have a good R and statistical analysis background (also with machine learning). in addition, I'm a fresh biotechnology grad. I would like to try to replicate some Rna-seq analysis with R papers (with ...
  • 31
1 vote
1 answer
29 views

Association analysis for methylation beta value and phenotypes in R

I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with ...
0 votes
2 answers
100 views

"Error in col2rgb(colors, alpha = TRUE) : invalid RGB specification" when running HeatmapAnnotation() (from ComplexHeatmap)

This question was also asked on github I'm trying to run the function HeatmapAnnotation (a function in the ComplexHeatmap package). When I run it, I get the error "Error in col2rgb(colors, alpha =...
  • 331
1 vote
0 answers
101 views

Missing value imputation method for gene expression data

I am new to working with gene expression data sets and am wondering what is the most standard or best way to impute missing values in a gene expression data? I got mine from the GEO database and the ...
  • 13
6 votes
1 answer
77 views

Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?

I am using the pairwiseAlignment function from the Biostrings package to calculate the distance between a consensus sequence and ...
  • 483
3 votes
0 answers
18 views

GRanges coverage error with discordant reads

I mapped my fastq files from 4SU-seq experiment to human genome hg19 with bowtie 2 and got this results: ...
2 votes
1 answer
22 views

Best way to match genes in two RNA-seq count matrices from two geo accessions

I have downloaded two datasets, and I am trying to remove the genes they do not share in common. Is there a biocmanager package with a function that can compare their gene ids, match them and reorder ...
1 vote
0 answers
14 views

Different output on same command and same input file, different library version

I am running a variant calling pipeline to detect solid tumours and haematological alterations. The variant calling is done with Mutect2, whereas I am using an R script to perform some filtering on ...
  • 243
1 vote
1 answer
124 views

How to consume non-CRAN packages in custom package?

In a custom package which imports a package from Bioconductor, what is the right DESCRIPTION file? I added in my DESCRIPTION a line with Remote like so ...
0 votes
0 answers
34 views

install a CRAN package that imports a CRAN package that imports a Bioconductor package

I have a CRAN package say myPack, that imports two CRAN packages, say cranA and cranB. These ...
3 votes
0 answers
31 views

How to identify in a RNA seq data in which sample is in which cell using R using qusage

I am using RNA seq data and have been using QuSage in R in hopes to try to identify different samples and figure out which cell it belongs to. I am trying to visualize and utilize the results but I am ...
1 vote
0 answers
27 views

Converting miRNA names to miRBase version IDs

I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example: hsa-miR-106a ---> hsa-miR-106a-5p hsa-miR-373* --> hsa-miR-373-5p hsa-miR-33 --> hsa-miR-33a-5p ...
  • 11
1 vote
1 answer
121 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
1 vote
0 answers
104 views

I can't launch FastqCleaner I always get a warning message and the application never starts

I tried to install all the needed and related packages but I still did not know what the problem is, Can anyone please help if anything else I can do?? I always get this over and over: ...
0 votes
1 answer
78 views

Accessing expression data in an ExpressionSet

I used rma from the oligo package to normalize CEL files, returning an object of class ExpressionSet. How do I access the actual ...
  • 1
0 votes
0 answers
244 views

How to get a consensus sequence from a nanopore fastq files?

I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed). I usually generate a consensus sequence with "...
0 votes
1 answer
50 views

Different results in differential expression analysis of microarray data

I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. When I run the code I get some different results in each time (about 50 or ...
  • 1
1 vote
1 answer
114 views

DESeq2. Which is better: using the altHypothesis argument in the results function or manually filtering for your desired P-value and Log2FoldChange?

In DESeq2 you can identify your differentially expressed (DE) genes using the results function. I noticed people in my lab using the results() function with the minimum number of arguments supplied (...
  • 13
2 votes
1 answer
95 views

ensembldb equivalent in python

Is there a python equivalent to ensembldb? I want to get genome coordinates for a transcript (like the function transcriptToGenome) but need to do it in python. I ...
  • 21
1 vote
0 answers
31 views

Is New Tuxedo approach really better than the earlier ones?

I am planning to perform multiple routine NGS analyses for a hospital lab on patients' samples on an everyday basis. Before I used a new tuxedo approach with ...
  • 103
5 votes
0 answers
105 views

Simultaneously get data from multiple applied gates in flowCore

Using the Bioconductor flowCore package, I'm applying two parallel and non-overlapping gates to a gatingSet directly under "root": ...
  • 183
0 votes
2 answers
48 views

Bioconductor Conda release delay

How long does it take for the latest Bioconductor to end up on Conda? I think I saw a blog post about the challenges with this process, but I cannot find it. For example, Bioconductor 3.13 was ...
  • 2,099
0 votes
1 answer
433 views

RDAVIDWebService (R package) manual installation, or alternative tool

Recently, I had to re-install all my R packages (R version 4.1.0 (2021-05-18) -- "Camp Pontanezen") and it turns out that "RDAVIDWebService" is ...
1 vote
0 answers
15 views

Bioconductor, genefilter() returns NULL dimensions, is my filtering process wrong?

I'm using R and bioconductor in order to conduct some gene analysis on an Affymetrix dataset (GSE173360) but I'm having trouble at filtering genes. I'm trying to create a dataset called small.eset by ...
  • 111
0 votes
2 answers
132 views

Determining what RNAseq data is filtered on volcano plot

I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
  • 1
1 vote
1 answer
75 views

Calling GEOquerry error while loading the library

Note: this question has also been asked on Biostars I started getting a strange error when trying to load GEOquerry with library(GEOquerry). ...
0 votes
2 answers
165 views

STRINGdb: reverse map STRING identifiers to gene names?

Is there a functionality within STRINGdb package or in another environment to reverse map the STRING identifiers to Gene names? For example, the entire STRING network can be downloaded using the ...
  • 428
1 vote
1 answer
124 views

Retrieving all genes for a gene ontology term

I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
  • 11
0 votes
0 answers
25 views

Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt

I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (https://f1000research.com/articles/4-1062#ref-21) which uses QuasR in the first step. My list of ...
  • 1
2 votes
1 answer
281 views

How do I include silent mutations in an oncoplot using maftools?

I have annotated files from annvar and I changed them into MAF by using annovarToMaf from ‘maftools’. Then I used read.maf to ...
's user avatar
5 votes
1 answer
835 views

installing multiple bioconductor packages at once

I was wondering if there is more elegant way of installing and loading multiple packages in Bioconductor similar to pacman with CRAN packages. I tried: ...
  • 75
1 vote
1 answer
91 views

Retrieve overlap widths with Bioconductor

I want to retrieve all overlaps between two sets of genomic intervals (GRanges) using Bioconductor. I am interested in the widths of the resulting overlapping ranges. In cases with discontinuous ...
  • 595
1 vote
0 answers
38 views

workflow for processed RNAseq data analysis in R [closed]

I'm learning to use R in data analysis. I'm getting fluent in baseR and the tidyverse, but thus far only dealt with medium throughput plate-based experiments. I am currently trying to learn how to ...
2 votes
1 answer
231 views

`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed

I think there is a problem with TxDb.Hsapiens.UCSC.hg19.knownGene and EnsDb.Hsapiens.v75. I'm struggling to install all of ...
  • 75
0 votes
1 answer
95 views

Get list of urls of GSM data set of a GSE set

I have this GSE dataset ( GSE104279 ) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279). I want to make a table with set IDs and ftp urls to use it as a table in galaxy.org I know that we ...
1 vote
1 answer
72 views

error in random forest analysis

I am now struggling to do random forest analysis, I will be thankful if you could help with code for random forest analysis. I got samples from the root, soil, and leaf from two regions (bau & mau)...
2 votes
1 answer
139 views

alpha diversity wilcox.test

I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column. ...
2 votes
2 answers
971 views

Python equivalent to R GRanges and IRanges

Problem: I am trying to convert some codes written in R to Python and part of that conversion process is find classes equivalent to the GRanges and IRanges from the GenomicRanges R package in Python. ...
0 votes
1 answer
105 views

How can I match sequences with IDs using python dictionaries?

...
  • 21
1 vote
0 answers
19 views

Questions about EBSeq (in R)

I have made a UMAP of malignant cells and the result is split into 3 clusters, as seen below. For the sake of example, let's say I want to find the differentially expressed genes in the uppermost ...
  • 11
1 vote
1 answer
145 views

Power calculation for GWAS/EWAS

I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease. I wonder, does anyone has came across ...
0 votes
0 answers
40 views

a proper Design Matrix for several drug treatments with both control negative and control positive

I have a dataset of RNA-seq samples for testing different drugs on the presence of another drug. One of my samples is the normal cells with no drugs (control negative) and another is the cells with ...
1 vote
1 answer
43 views

DiffBind, diffferentially binding site

I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates. when I run the diffBind package I have three contrast: ...
  • 95