Questions tagged [bioconductor]
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
185
questions
19
votes
2
answers
10k
views
Understanding DESeq2 design, contrast and results
I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 ...
- 3,090
18
votes
2
answers
10k
views
How can I extract normalized read count values from DESeq2 results?
The results obtained by running the results command from DESeq2 contain a "baseMean" column, which I assume is the mean across samples of the normalized counts for ...
- 3,090
17
votes
4
answers
2k
views
Why Bioconductor?
What are the advantages of having Bioconductor, for the bioinformatics community?
I've read the 'About' section and skimmed the paper, but still cannot really answer this.
I understand Bioconductor ...
- 2,624
16
votes
3
answers
5k
views
R package development: How does one automatically install Bioconductor packages upon package installation?
I have an R package on github which uses multiple Bioconductor dependencies, 'myPackage'
If I include CRAN packages in the DESCRIPTION via Depends:, the packages ...
- 1,681
13
votes
2
answers
3k
views
Are fgsea and Broad Institute GSEA equivalent?
Several gene set enrichment methods are available, the most famous/popular is the Broad Institute tool. Many other tools are available (See for example the biocView of GSE which list 82 different ...
- 4,692
10
votes
1
answer
2k
views
Intersection of two genomic ranges to keep metadata
I am trying to find intersection of two genomic ranges (gr1 and gr2) and keep metadata from one of them
...
- 203
10
votes
1
answer
2k
views
How to manipulate protein interaction network from String database in R?
How can I manipulate protein-interaction network graph from the String database using STRINGdb bioconductor package and R?
I have downloaded the whole graph for ...
- 103
9
votes
3
answers
2k
views
How to identify gene expression signatures from gene expression data?
I have TCGA gene expression data. I'm interested in identifying gene expression signatures using the data.
I would like to know whether there are any tools or R packages for identifying gene ...
- 1,262
9
votes
2
answers
1k
views
Duplicate genes with RSEM counts: Which one to choose?
I have Ensembl ids in the first column and samples with RSEM counts data in other columns. I converted Ensembl ids to gene symbols. Now I see there are three genes repeated twice.
...
- 1,262
8
votes
3
answers
507
views
What are the ways to keep track of branches in the analysis?
I'm going through an RNA-seq pipeline in R/Bioconductor and want to try multiple parameters at subsequent steps, for example, running clustering with different ...
- 2,624
8
votes
1
answer
7k
views
Extracting expression data from GSE dataset downloaded from GEO
I have downloaded GSE16146 dataset from GEO using GEOquery R package.
I would like to extract "Data table" from downloaded GSE16146.
...
- 81
8
votes
2
answers
80
views
Melt p-values for CpG sites mapping to the same gene
I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
- 81
7
votes
1
answer
1k
views
How can I colour boxes in Gviz AnnotationTrack in R?
I'm learning the Gviz bioconductor package, I generate a plot as follows:
...
- 3,928
7
votes
1
answer
1k
views
Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids
I have a matrix of gene counts which I'm going to use as input for DESeq. Right now, each gene is labeled by its Ensemble transcript ID, but I'd like to convert these to their HGNC symbols before I ...
- 541
7
votes
1
answer
463
views
Get RefSeq accession numbers with versions
Google searching for NM_002084 gives the following result:
NM_002084.4
This, I assume, is the latest version v4, hence the .4 suffix.
Searching for previous ...
- 1,042
6
votes
3
answers
1k
views
How to subset a GRanges via an argument passed into a function?
Let's say I have following example GRanges:
...
- 1,393
6
votes
2
answers
2k
views
Running differential expression analyses on count matrices with many zeroes
Note: I also posted this issue (with less context) in the bioconductor support site: https://support.bioconductor.org/p/97424/
I'm working on a snakemake workflow that identifies various small RNA ...
- 3,090
6
votes
1
answer
61
views
SNP located within a promoter region (pig)
I have a couple of SNP identifiers such as MARC0073381 or ALGA0066960. The corresponding platform is Illumina Porcine SNP60 BeadChip (WG-410).
I want to know if these SNP are located within a ...
- 61
6
votes
1
answer
565
views
How to find hairpin loop structure in a large set of long non coding RNA transcripts
I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding ...
- 341
6
votes
2
answers
962
views
Transcript Coordinate Ranges to Genomic Coordinates
I have 2 GFF3 files:
Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space.
Features using chromosome IDs as the landmarks. i.e. "exon" ...
6
votes
2
answers
134
views
Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?
Update: I submitted a pull request to the Biostrings repo. The functionality I describe in my question and answer can now be implemented with ...
- 603
5
votes
3
answers
453
views
Is there an efficient way to check an input BAM in R?
I'm writing a function in R for an R package which takes as input a BAM.
...
- 1,393
5
votes
2
answers
365
views
Is there a Python/R package with the ability to convert an alignment and reference into a CIGAR?
I'm writing a python function from scratch to do this, but I feel like this must exist in some standard bioinformatics library already. In principle, this is a simply regex operation which many must ...
- 1,393
5
votes
2
answers
7k
views
Ensembl id to GeneSymbol with biomart
I have 3224 Ensembl id's as rownames in a dataframe "G". To convert Ensembl ids into Genesymbols I used biomart like following.
...
- 1,262
5
votes
1
answer
2k
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:
...
- 175
5
votes
3
answers
123
views
Sampling haplotypes
I am trying to simulate different genome of peoples, I have data (VCF files) of various genes from the 1000K Gene project.
I want to simulate different whole genomes i.e generate a new population by ...
- 231
5
votes
1
answer
226
views
Obtaining data table headers from GEO using GEOquery
For a study in GEO, I would like to obtain the data table header descriptions, specifically the "VALUE" column for all samples in the study.
If you go here: https://www.ncbi.nlm.nih.gov/geo/query/acc....
- 83
5
votes
1
answer
808
views
Voom function from limma package and Normalization on counts data
I know that Voom function from limma package from Bioconductor converts raw counts into log-CPM values and then Normalization is applied on that, with normalize.method argument.
I would like to know ...
- 1,262
5
votes
1
answer
117
views
How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?
I have crossposted this question in maths StackExchange. The problem is dominantly mathematical (this question) but the application of the problem is mainly biological. Hoping that people in this ...
- 200
5
votes
0
answers
156
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
5
votes
0
answers
208
views
R Biostrings pairwiseAlignment to BAM
The R package Biostrings has a function to create a pairwiseAlignment from pattern and subject sequences.
So far I can save the result into a text file using writePairwiseAlignments. I would like to ...
- 151
4
votes
1
answer
16k
views
Error in as.vector(x) : no method for coercing this S4 class to a vector
I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error:
<...
- 351
4
votes
2
answers
909
views
Normalizing microarray data for clustering heat map
I wanted to generate a clustering heat map for the microarray data. This is the first time I'm working on Microarray data. I read some tutorials but have few doubts.
I'm using microarray (Affymetrix ...
- 631
4
votes
1
answer
130
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 ...
- 205
4
votes
2
answers
9k
views
RNAseq: Z score, Intensity, and Resources
I'm very new to bioinformatics in general, and I'm trying to understand some basic concepts.
I have RNAseq data, and bioinformatics people tell me that intensities cannot be compared across patients. ...
- 401
4
votes
1
answer
253
views
How should I address batch effects in my experiment?
Let's say I have an RNA-Seq experiment, where I'm interested in the significantly differentiated genes between pre-treatment and post-treatment conditions. "rep" == biological replicate.
...
- 2,739
4
votes
1
answer
15k
views
changing color key range to specified range in heatmap.2 function
I have a tab separated text file as shown below
...
- 420
4
votes
1
answer
2k
views
10x Genomics Chromium single-cell RNA-seq data analysis options?
Provide an overview of 10x data analysis packages.
10x provides Cell Ranger which prepares a count matrix from the bcl sequencer output files and other files (see bottom of page https://support....
- 2,624
4
votes
1
answer
3k
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 ...
- 1,993
4
votes
1
answer
205
views
How to find genomic overlaps faster?
I was trying to find a way to find overlaps between two genomic ranges. I found a post at Biostars but it couldn't consider the chromosome information. For example:
...
4
votes
1
answer
1k
views
Hierarchical models with limma?
I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
- 195
4
votes
1
answer
139
views
Standard Cutoff for Moderated T-statistics
I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma.
Is there any standard practice for where to cut off that value? For log2 fold change I ...
- 401
4
votes
1
answer
355
views
Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?
Let's say I have the genome hg19 loaded into R via BSGenome
...
- 1,681
4
votes
1
answer
355
views
How to extract gene expression tables from this GEO dataset?
I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene ...
- 79
4
votes
1
answer
275
views
Installing RnBeads via bioconductor - .onLoad failed in loadNamespace(), call: NULL
I am trying to install RnBeads from bioconductor but the installation of its dependancy TxDb.Hsapiens.UCSC.hg19.knownGene fails. ...
- 116
4
votes
1
answer
214
views
Problems in creating desired phylogenetic tree with ggtree
I am working on haplotype data and want to make a tree out of haplogroups using ggtree. I have following data in newick format.
...
4
votes
1
answer
144
views
Counting the number of paralogues for mouse genes gives me the wrong frequency in R
I am trying to count the number of paralogues for the mouse homologues of the human protein-coding genes using BioMart. But for example in the 'PLIN4' gene its counting 35,000 paralogues instead of 4. ...
- 49
4
votes
0
answers
292
views
R package equivalent to RSeQC infer_experiment to get strandedness of RNA-Seq
I am currently writing an R package that includes a module to run featureCounts (gene quantification tool) from Rsubread. I wanted to be able to specify the correct strandedness option to ...
- 41
3
votes
1
answer
6k
views
How to transform a DNAStringSet from the Bioconductor package Biostrings to a data frame?
I am working on Mac OS X. I am using R version 3.5.1.
I have important a FASTA file into R using Biostrings::readDNAStringSet. This creates a DNAStringSet object ...
- 2,459
3
votes
3
answers
3k
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 ...
