5
votes
Converting Chip-seq fastq format ({$x_k$} list of seq segments) to genome browser {sequence $x_i$, count-number $y_i$} format
I have no idea about what you are actually trying to achieve, but getting these browser tracks is simple. First you align your fastq files to a reference genome, e.g. with ...
3
votes
Sanger Sequencing Knitting Error
Your code runs without error on my laptop (macOS 13.2.1; R v4.2.2; Rstudio 2022.07.2), so I have some further questions that might help with troubleshooting (too many to include in a comment):
Does ...
- 500
3
votes
file path of BiocManager:install()
First, I would try again to download via the bioconductor command. If your internet is intermittent it may just take a few tries.
If that doesn't work, I would then strongly recommend using ...
- 3,429
3
votes
BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code
The previous answer is correct, in that the compiler wants to be able to use C99 to compile your library.
However, the solution of putting ...
- 1,482
2
votes
beginner RNA-seq Replicate papers
I like Gierlinksi, et al., Bioinformatics, 2015 for this type of problem.
I like this paper because the methods are descriptive and clear, they have lots of figures that you can reproduce along the ...
- 1,364
2
votes
Accepted
Common tools for generating results and visualizations for bioinformatics and genomics publications
Figure 1A: These genome browser snippets are either plain screenshots from applications like IGV or created from within R with software like gviz.
Figure 1B: This looks like base R plotting routine. ...
2
votes
Unable to install an R Bioconductor package on Apple M1/M2
The easiest solution is to install the x86 version of R in your M1/M2 Mac here.
It will be then emulated by the Rosetta. After that you will have no problems with Bioconductor packages
- 214
2
votes
Keep first 20 nucleotides of sequences using R
You will need to "read" your data. There are packages that can read Excel files directly but I would save the data as csv first and then use read.csv(). ...
- 3,692
2
votes
include a glimma interface in a shiny app
I have come across this page today with same query. After visiting here and there, finally following approach helped to resolve this issue. I must confess that I am just a beginner to R Shiny.
Lets ...
2
votes
Error while using SummarizedExperiment() in R
DESeqDataSetFromMatrix but a SummarizedExperiment is not a matrix. Use the function DESeqDataSet() instead and make sure the ...
- 551
1
vote
How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?
Checkout an MSA visualisation and analysis package that you can load the alignment into. It may not be the newest tool, but I've used Jalview (https://www.jalview.org/) in the past
- 3,878
1
vote
Error in dimnamesGets(x, value) when trying to read data using Seurat package
There is a mismatch of 1 line between the several files, suggesting that probably either the barcodes of features file has a header line which is not standard. Remove any header lines from these files....
- 11
1
vote
Error in dimnamesGets(x, value) when trying to read data using Seurat package
Check the length of your files. The error clearly says that there is a difference in the length of your files. Your file length should be equal.
I think the problem may be the presence of a header in ...
- 193
1
vote
Accepted
BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code
You can set a specific compiler in ~/.R/Makevars file, create the folder and write it down in Makevers:
CC = gcc -std=c99
or:
<...
- 769
1
vote
Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?
Additional answer on asymetric IUPAC score matrix.
To get the scores with an asymentric score matrix. This is also implemented in the Bioconductor package MSA2dist (https://www.bioconductor.org/...
- 11
1
vote
Accepted
Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?
Background
I've dug into the source code for the nucleotideSubstitutionMatrix() function from the Biostrings package. Here is ...
- 563
Only top scored, non community-wiki answers of a minimum length are eligible