Questions tagged [bioconductor]

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

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18 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 ...
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27 views

How to understand time-course gene expression plots with boxplots?

About time-course gene expression data, I need to understand these boxplots on the fig. 3. I just have tried to replicate the author's experiment for one compound using Bioconductor's limma package ...
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1answer
55 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)...
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1answer
35 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. ...
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10 views

Methods to analyze MeDIP-seq data

I have MeDIP-seq data. I have 6 groups with 15 replicates and a total of 90 human samples. I am trying to choose the best method to analyze them. I would highly appreciate if you can give me your ...
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1answer
86 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. ...
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54 views
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15 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 ...
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1answer
60 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 ...
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34 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 ...
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20 views

particular heatmap combinning to barplot for up and down-regulated genes

I have a list of genes (regulated up and down) by Deseq2 . I'd like to generate a heatmap of a particular combination for the barplot like in this graph : which I read in this paper: https://www....
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1answer
23 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: ...
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3answers
338 views

How to reduce the occupied RAM when you are dealing with a very sparse matrix in a single-cell Experiment in R?

I'm dealing with a very large and sparse dataset and the first issues I met occurred when I tried to use quickCluster that reported me this error: ...
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28 views

Is there a way to customize what observations are plotted in ComplexHeatmap?

So right now my observations in the dataset I've processed is stored as sample identifier columns and gene rows: an example of this would be for sample 1 and gene TRIM21 the observation is Missense ...
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1answer
48 views

Plotting metadata from GenomicRanges object

I have a GRanges object with metadata that I want to plot. Many of the online tutorials which manipulate these GRanges for plotting show how to plot the main columns (chromosome,start/end,strand) but ...
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25 views

Grabbing all Immune related genes with databases in R

I am having trouble grabbing specific pathway info using databases in R. I have RNAseq results and I want to remove immune related genes from the current list that I have. With a vector of gene ...
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1answer
55 views

WGCNA co-expression network analysis with less than 20 samples

I have two cancer subtypes data. Subtype A is 14 samples and Subtype B is 23 samples. I'm interested in identifying the functions of some LncRNAs in the Subtype A group. For this I'm using all protein-...
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21 views

Convert Data to be suitable for M3Drop did not work

When I try to convert data to use with M3Drop, I get the error message shown below. Does anyone know the reason and how to deal with it? Thanks! ...
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1answer
58 views

PCA plot did not work in single cell RNA-seq

I run plotPCA for single cell RNA-seq data, while I get error message (I use R 4.0). I attached the code and error message here. Did anyone know the reason and how to deal with it. Thanks! ...
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2answers
236 views

calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use calculateQCMetric function to calculate the quality metrics, but I am getting ...
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1answer
46 views

Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19)

I have a problem in R. I have the following dataSet (the first three rows shown) (the 5th number is the methylation level in its region): ...
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2answers
307 views

isSpike function in SingleCellExperiment package is deprecated?

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use isSpike function to filter out ERCC (control) and MT (mitochondrial RNA) reads, ...
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1answer
141 views

Using bioconductor from Python

Has anyone used bioconductor from Python? Is there any reason I would choose to use it from R instead of Python? It seems like there is a Python extension for it. Also, is there any reason to use ...
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224 views

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘“SeqFastaAA”’ to a data.frame

The example that I am trying to follow is this PGA tutorial. I want to use the information in the analysis of the mzML raw files from the proteomics data analysis. When I try to load the fasta file, I ...
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2answers
33 views

Identify differentially covered genes only between two samples

I have a question about finding differentially covered regions (coverage represents methylation level which goes from 0 to several thousands). I'm using enrichment based method which can be summarized ...
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30 views

reactomePA dataset

I tried to create my geneList according to this r code: setwd("C:/cygwin64/home/DIANGO/EXCELL/") d = read.csv("PA_down_id.csv",sep = " ", header = F) head(d) ...
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1answer
33 views

Is there a tool for synonymous recoding of DNA sequences?

I've got a DNA sequence that I'd like to make synonymous mutations throughout, thereby preserving the amino acid sequence. Does anyone know of a tool to achieve this
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1answer
36 views

How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic)

The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on ...
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1answer
71 views

qvalue and p.adjust functions

Between the qvalue package and the p.adjust function, which is more appropriate to use when trying to calculate the q-values of a dataset? According to the manual for the q-value package, the q-value ...
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1answer
36 views

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted BAM files?

I have called peaks using MACS2 and now I'm trying to run ChIPQC bioconductor package. Can someone please tell me should I use sorted BAM files or unsorted BAM files? I have created sorted BAM files ...
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1answer
66 views

Can I submit a R package to Bioconductor or CRAN if I have already published it a journal?

I have written a bioinformatics package in R that I want to publish in a bioinformatics Journal. Presently, I am maintaining a local repo of that package and I want to put in the Bioconductor ...
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1answer
25 views

Error in createMAE function: non-unique values when setting 'row.names' in TCGA LIHC Data

I am working with the createMAE() function of the ELMER Bioconductor package. While executing the createMAE() function using ...
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2answers
291 views

Making a volcano plot look less cluttered

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
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0answers
90 views

Error in my RNAseq analysis

I was following the RNAseq analysis tutorial online(https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html) but am not obtaining the same variance values for each row in the logcounts matrix....
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46 views

include a glimma interface in a shiny app

I am trying to code a shiny app for RNA-Seq data analysis. I would like to include glimma interactive plots in it. However, in my current interface, clicking the action button ...
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23 views

Geneoverlap library data input

GeneOverlap I am trying to use this library so in the default data sets it has different list of genes which are categorized as high low or medium expressed genes. So my question is can I run this one ...
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11 views

co-expression between LncRNA and mRNA based on P.value and correlation

I have two sets of data, each of which has two treatments with two replications. The first group consisted of 2261 LncRNA (Long non-coding RNA) with FPKM each LncRNA and the second group consisted of ...
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2answers
76 views

What kind of analysis is practically done on GSE data files?

I have a GSE data file in csv file format containing fields such as: ID, adj.P.Val, P.Value, t, B, logFC, Gene.symbol, Gene.title. In which adj.P.Val, P.Value, t, B, logFC fields being numeric. What ...
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2answers
68 views

How can I find all the columns available in UniProt.ws package for R?

I am trying to find the subcellular localization of my 10,000 proteins using UniProt.ws package for R. However, I am unable to find all the columns available for query. I used another package named ...
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2answers
94 views

GenomicRanges: get nearest neighbor distances for random genes using a for loop

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this: ...
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0answers
39 views

Row labelling in a heatmap in R

Could I have specific row labels in bold text but not all of them when creating a heatmap using R? (eg. using heatmap.2 function)
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1answer
68 views

I have a list of protein targets. How to get structural data (atomic coordinate) from PDB?

I have a list of around 500 protein targets (human). I only have their protein symbols. As an example: EGFR AR FOXA1 CXCR3 ... I want to get structural data (atomic coordinate) from PDB (Protein ...
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1answer
73 views

After running a DRIMSeq pipeline, how do I know which genes are upregulated in the different conditions?

After running a DRIMSeq pipeline and obtaining the genes that are differently used between the null and full models, how do I select the genes that are differently used in the different conditions? ...
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14 views

GEOquery, Bioconductor question: Is there a more efficient way to tease out datasets that contain data I need?

We are doing a study analyzing the expression of certain genes and correlating that with response to chemotherapy. So far I have been manually going through every dataset on the NCBI website and ...
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36 views

Mapping GPL Platform Number to Microarray Name

I am trying to download a dataset from GEO using the GEOquery R package. Using this package, I can retrieve the GPL platform number(s) for the dataset, and I hope to use a CDF file from BrainArray on ...
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1answer
782 views

Using `install.packages` with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific ...
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1answer
33 views

Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment that will lead to the ...
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1answer
190 views

Error: package or namespace load failed for 'ChIPseeker'

How do I solve the problem of loading the bioconductor Chipseeker package? I have installed in the following way and I having an error while loading it and I do not know why. ...
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2answers
217 views

Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?

I would like to visualize tree with multiple sequence alignment. My din.newick file is shown below, ...
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3answers
114 views

Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column

I have a "test" data.frame object in R, which is basically a small subset of a 66000 row dataframe, which looks as follows: ...