Skip to main content

Questions tagged [r]

Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackexchange.com.

Filter by
Sorted by
Tagged with
0 votes
2 answers
825 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 =...
Lou_A's user avatar
  • 361
2 votes
1 answer
333 views

baseMean threshold

I have an RNA-seq dataset and I am using DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have ...
suzie321's user avatar
1 vote
0 answers
134 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 ...
b14108's user avatar
  • 13
2 votes
0 answers
292 views

Subsetting with harmony

Currently merged two Seurat objects together and then ran Harmony for batch correction. Now I want to subset out a cell type of interest do I re run harmony or just do the standard PCA? ...
mmpp's user avatar
  • 371
2 votes
0 answers
248 views

Subsetting out prefix from genes and merging

I'm working with PTX samples (human and mouse), they're aligned to both transcriptomes and so gene names contain hg38- and mm10- at the beginning of each gene. I have eliminated teh prefixes because I ...
mmpp's user avatar
  • 371
6 votes
2 answers
162 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 ...
acvill's user avatar
  • 613
0 votes
0 answers
43 views

Problem of writing scilab code on a project - Morris-Lecar model

This is a computational neuroscience project. We are asked to plot the Morris-Lescar model (question 3 below). The model should be plotted with scilab or R. however, I don't know where to start? For ...
ApplePie's user avatar
3 votes
1 answer
2k views

Grouping x-axis in scatter plot

I am trying to plot one scatter plot for each group, where each group has continous values in x-axis. Reference Data Gives continuous x-axis but all groups are combined. ...
user98059's user avatar
  • 347
2 votes
0 answers
58 views

open source tools for CNV analysis from illumina SNP array

What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well. I'm working with leukemia sample and ...
newbiocoder's user avatar
0 votes
0 answers
3k views

DimPlot - How to highlight cells with identity colors?

I made this wrapper for DimPlot: ...
Johnny Rocketfingers's user avatar
3 votes
0 answers
32 views

Is there a generally accepted method used to impute missing DNA methylation data (probe beta-values)?

I'm looking at DNA methylation (DNAm) data such as TCGA (e.g., BRCA, KIRP, KIRC, etc.). Currently trying to build use my model to predict DNAm age on test sets, but many of the data sets are missing ...
sumthymes's user avatar
2 votes
0 answers
87 views

Pulling out genes in a scatterplot

I'm comparing gene expression among 2 different datasets (in vivo and in vitro) I have made a heatmap showing the correlation for each and then plotted the data frame to create a scatterplot. Now I ...
mmpp's user avatar
  • 371
3 votes
0 answers
77 views

LRT test in deseq2 on multiple condition

I have some doubts when i'm running LRT This is my condition data-frame small subset ...
kcm's user avatar
  • 1,804
3 votes
1 answer
485 views

Constructing Two Triangle Heatmaps in One Square

I'm looking to make a two, two range colour scheme heatmap where each range corresponds to a separate triangle in the heatmap square. I am looking for a relevant guide for this heatmap. Any ...
raysteven's user avatar
3 votes
2 answers
475 views

Wrapping R scripts in WDL and run in docker

I am trying to run an R script as a task in WDL in a docker image. Since this is my first time working with these, I am stuck in something very simple (and in the initial stage) and am hoping somebody ...
binn's user avatar
  • 73
1 vote
1 answer
90 views

A two color bar plot in R

I have raw read counts of miRNAs in two conditions like below ...
Zizogolu's user avatar
  • 2,160
0 votes
0 answers
47 views

Error in as.character.default(new("BSgenome", pkgname = "BSgenome.Hsapiens.UCSC.hg19", : no method for coercing this S4 class to a vector

I am trying to use the following function in R: ...
Minh Tris's user avatar
0 votes
2 answers
30 views

subsetting more than one ccle sample

I'm working with the CCLE dataset and I'm trying to subset the data to just 3 cell lines of interest but not sure how to it. Currently, I have been subsetting one by one but is there an easier way? <...
mmpp's user avatar
  • 371
-1 votes
1 answer
947 views

Selecting a part of heatmap

I have a heatmap I see a block of genes for a group of samples How I can select a part of heatmap? I mean is there any way to export a list of genes from rows of a heatmap in R? I have tried which ...
Zizogolu's user avatar
  • 2,160
3 votes
2 answers
2k views

How to subset a GRanges object based on a specific genomic window of interest?

Goal: To keep only rows of a GRanges object if their start coordinate is within 1 Mb of the start coordinate of a gene of interest. I am aware of some functions that come close: ...
Gawain's user avatar
  • 315
3 votes
2 answers
938 views

Plotting a gene in Seurat

I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice. <...
Angus Campbell's user avatar
2 votes
2 answers
2k views

Featureplot by co-expression of some genes

I want to identify MDSCs cells which don't not express HLA-DRs (HLA-DR negative) but express ...
Zizogolu's user avatar
  • 2,160
2 votes
1 answer
57 views

Displaying BIC and AICs from MSA nucleotide multisequence fasta file

I am initiating a project reproducing MEGA style trees using R to find the best DNA protein models under AIC/BIC. I have read the R AICs and BIC documentation but I'm struggling to implement this. ...
brudernihil's user avatar
1 vote
0 answers
36 views

Separation of dihedral angles of the desired sequence in the protein

have a list of pdbid and I want to separate the dihedral angles of some sequences in protein . ...
user18043726's user avatar
1 vote
0 answers
16 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 ...
BCArg's user avatar
  • 283
1 vote
2 answers
556 views

How to input data and metadata from NCBI for RNA-Seq analysis in R

So, I have downloaded some .txt and .csv files containing the raw count data (I am supposed to find out differentially expressed genes and see which genes and up- and down-regulated). I have also ...
Addy's user avatar
  • 11
3 votes
1 answer
1k views

In a RNA-Seq heatmap should you do Z-score standardisation before clustering the rows/columns or after?

I have made a heatmap using RPKM values from a RNA-Seq dataset using the pheatmap() function in R. I have log2-transformed the data before performing Z-score standardisation of the data. I have also ...
ceno980's user avatar
  • 159
0 votes
1 answer
286 views

How to remedy a DESeq2 collapsing technical replicates error?

Goal: To ensure "the sum of the counts for [my samples] is the same as the counts in the [samples] columns in ddsColl" after collapsing replicates using ...
Gawain's user avatar
  • 315
1 vote
0 answers
75 views

How can I get a column with real gene names in my ballgown analysis?

I am doing RNAseq analysis and I am using ballgown procedure for it. There is an option in R to calculate differentially expressed genes and use FPKM in calculating differential gene expression, which ...
Mark's user avatar
  • 103
1 vote
1 answer
688 views

RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?

I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code: ...
ceno980's user avatar
  • 159
0 votes
0 answers
48 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 ...
Stefka Asenova's user avatar
0 votes
2 answers
61 views

How Does Cox Proportional Hazard Model Describe Interaction between Covariates

I have read STDHA and the documentation for the coxph() function in R. I understand that the cox PH model explores how different covariates simultaneously impact survival. Based on the Lung data ...
dunkindonts's user avatar
1 vote
1 answer
1k views

Best methods for clustering heatmap based on regions where the genes are most highly expressed?

I am analysing RNA-Seq data for a set of genes from different human brain regions using data from the Allen Brain Atlas. I have made a heatmap using GraphPad Prism. In this heatmap, I show the average ...
ceno980's user avatar
  • 159
1 vote
2 answers
717 views

Reading in external single cell data

I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix. counts found here: https://www.ncbi....
mmpp's user avatar
  • 371
1 vote
1 answer
618 views

maxEE parameter from DADA2 package in R

I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails. I have surfed many forums, as well as the details given by ...
h3ab74's user avatar
  • 846
0 votes
1 answer
154 views

Calculating dn/ds ratio between two model organisms

I am trying to calculate the dn/ds ratio between the human genes and c.elegans. However, I am getting NA values in the output file I used the following script ...
Tom Morgan's user avatar
0 votes
0 answers
153 views

Error generating count data using featurecounts in R

I am doing some RNA analysis and am having issues trying to generate count data. I mapped my reads to a reference genome fasta file (genbank fasta file from ncbi) using bbmap and .sam files as the ...
user14648's user avatar
3 votes
0 answers
33 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 ...
Rachel 's user avatar
2 votes
1 answer
9k views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
Zizogolu's user avatar
  • 2,160
1 vote
0 answers
42 views

How to split genotypes into two groups from a SNP txt file contains -1, 0 and 1 in R?

I have a SNP file(it is 96 obs. of 1178 variables with -1, 1 and 0 and in some places NA) and I need to calculate Jaccard genetic distance from them in R. Is there any way to convert these 3 values to ...
coxtheparadox's user avatar
-1 votes
1 answer
80 views

Visualizing top expressed genes

I have a spreadsheet of CPM values I want to visualize the top 20 genes expressed across my samples This is how my data look like ...
Zizogolu's user avatar
  • 2,160
0 votes
1 answer
191 views

How to extract part of protein complex separated with HEADER with two molecules from one PDB file

I have a PDB file which contain two molecules (receptor and ligand). Each molecule will have its own header. All in ONE PDB file. ‌The header of receptor section looks like this (line 1-6 of the PDB ...
littleworth's user avatar
1 vote
0 answers
88 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 ...
Sadaf's user avatar
  • 11
1 vote
1 answer
2k views

FindMarkers from Seurat returns p values as 0 for highly significant genes

I have been working on FindMarkers function for identifying significant genes in the cluster. But some Significant genes have very low p values, so they are returned as 0 in the output.Any value less ...
Austin George's user avatar
0 votes
1 answer
2k views

How to extract the protein sequences of a genbank file using R or biopython

sorry for the question, I'm trying to extract the proteins sequences from a genbank file. ...
abraham's user avatar
  • 115
0 votes
0 answers
123 views

Linking UK biobank patient IDs with their corresponding genetic data

I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs. I am trying to test with chromosome 5 as I have both bgen ...
Muhammad's user avatar
1 vote
0 answers
49 views

The correct design for time series experiment

I have a treatment and control in two time points like this ...
Zizogolu's user avatar
  • 2,160
1 vote
1 answer
166 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
Leon Lenzo's user avatar
0 votes
0 answers
35 views

Error in "apply(grps, 1, function(x) any(is.na(x))) : dim(X) must have a positive length" at running dht2 function in R

I am running the script from de Distance examples (http://examples.distancesampling.org/Distance-cues/cuecounts-distill.html) to estimate density using function dht2 of Distance library but I have an ...
Esperanza's user avatar
1 vote
3 answers
483 views

R help in Jupyter notebook?

I'm using this Jupyter notebook to work on R... How do I do the equivalent of ?someFun? When I run that in the notebook, I get: ...
Dan Bolser's user avatar

1
3 4
5
6 7
19