Bioconductor Forum

HELP?   I am working on a project and have a list of genes I'm looking at.  I would like to generate a random control list of genes that has the same number of genes and approximately...the same coding length as my gene list of interest.  Is there anything in bioconductor that can do this.  The basic question is:  "Is...the number of variant…

random generator gene list

updated 7.7 years ago • paul.hillman

I'd like to know if it exist a command or a package that can help me to retrieve the aminoacid sequence starting from the protein identifier, through a link with Uniprot or similar: Let's say I have : P10451 , Human I would

updated 16.6 years ago • Giulio Di Giovanni

function that would calculate the expected value/frequency of finding a subsequence, within a sequence of length L. For example, assuming that all nucleotides are equally probable, how many times would we expect to find...the pattern 'ATTG' in a sequence of length = 20. I tried looking in biostrings and IRanges, but didn't find what I was looking for. many thanks! [[alternative

Biostrings IRanges Biostrings IRanges

updated 12.9 years ago • Tim Smith

I am creating my annotation package using makeOrgPackage(). I followed the instruction here: http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Forge/inst/doc/MakingNewOrganismPackages.htm This are the dataframes and the commands I used: > test3 GID Gene Name Protein Name 1 PSE\_0724 PSE\_0724 GCN5-related N-acetyltransferase 2 PSE\_0725 PSE\_0725 GCN5-related N-ac…

annotationforge Annotation GO

updated 11.3 years ago • artur

class="preformatted">Hi, there; I am new to bioconductor, thus I have a simple question. How to get gene names in arabidopsis array, I can get affyID, but hope to get gene name or find affyID for a list of genes. I tried > getSYMBOL

updated 21.4 years ago • Fangxin Hong

isn't it? Another problem is the case where 10 probesets are supposed to interrogate a particular gene and one is significant, but the other nine are not. In that case is the gene differentialy expressed or not? What you have...cdfs discard the original probesets and only use those probes that are known to map to unique sequences in the genome (based on the current UniGene build), and then map to…

Microarray Cancer hgu133plus2 probe affy limma gcrma Microarray Cancer hgu133plus2 probe

updated 18.4 years ago • Chunyan Liu

Hi, I am using tximport to combine the gene-level quantification and further normalize it using edgeR's TMM normalization. The code I used is from https://bioconductor.org...vignettes/tximport/inst/doc/tximport.html#edgeR ```r cts <- txi$counts normMat <- txi$length # Obtaining per-observation scaling factors for length, adjusted to avoid # changing the magnitude of the …

tximport edgeR

updated 2.4 years ago • hanc

Hello, I need to map GenBank protein ID's to corresponding Uniprot ID's from non-model organisms (e.g. ACF95883.1 = https://www.uniprot.org/uniprotkb/B5ATG2/entry = SOX9). I am struggling

UniProt.ws AnnotationDbi

updated 18 months ago • georgii.vdovin

Hello All, I am preparing to run normalization and differential expression on my RNA sequencing raw counts data. However, I wanted to perform a gene filtering step before running limma for batch correction (16...were used for data collection) and DESeq2 (DE Analysis and Normalization). I started with ~60,000 genes and I have already filtered for removal of genes was greater than or equal to 5…

DESeq2 limma RNAseq

updated 22 months ago • kcarey

use RSubread's `cellCounts` function to process a scRNAseq dataset but am encountering an error. We sequenced the same sample on two instruments: 1. Illumina NextSeq 500 (28 + 56 nt) 2. Illumina NovoSeq 6000 (150 + 150 nt) The `cellCounts...memory mapping error on the NovoSeq instrument (at 150 + 150 nt): ``` || Sort the 28395 genes... …

Rsubread

updated 23 months ago • Joe Marturano

in replicate.  One question I have is how to handle the situation where only one 4-bp cutter enzyme was applied (DpnII) and not two different enzymes like in standard 4C-seq applications.  Do I enter the  DpnII...recognition sequence (GATC) twice for both reSequence1 and reSequence2?  Since Capture-C uses 160 bp biotinylated probes for capture...vs an inverse …

fourcseq

updated 7.6 years ago • mmackiewicz

showthread.php?t=35472#6 Like honey bee, B. subtilis (bsu) is not a major species with Bioconductor gene annotation package as those listed in data(bods) under pathview package. similarly you need to map Locus_tags to Entrez...expression changes with Pathview. But I have a problem. We got Locus_tags like BSU00010 and no gene IDs and I don't know whether Pathview can use it or not. I really do…

Microarray Annotation Bacillus subtilis gage pathview Microarray Annotation gage pathview

updated 12.0 years ago • Luo Weijun

div class="preformatted">Dear list, can anybody suggest how could I insert gene names in additional to gene symbols on my topTable generated by limma with my differentially expressed genes? cheers

limma limma

updated 16.3 years ago • Marcos Pinho

When I use summarizeVariants with a GRangesList of genes, the genes are then reordered in the RangedSummarizedExperiment object and the assay(counts) values are incorrect...a bug or can I control this reordering?   <pre> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene genes <- genes(txdb) # get the gene symbol for corresponding ENTREZID gene.map &a…

variantannotation summarizevariants

updated 8.6 years ago • Todd Creasy

the KEGGgraph package to plot pathways with moderate success. When I am working with ~100 nodes, the gene names are included on my final plot. However, when I have larger datasets (~300 nodes) the names disappear. I am using the same...method to obtain gene names and the same parameters to add them to the plots. Does anyone know how to solve this? ```r ##Plot parameters nA <- makeNod…

KEGGgraph

updated 2.6 years ago • hilarius_bookbinder

I have published \`RTCGA.rnaseq\` R package that provides datasets from TCGA project containig RNA sequencing (gene's expressions). I am wondering if there is a way to change this package name to be more proper like \`RTCGA.RNAseq

r developers devel

updated 10.2 years ago • MarcinKosiński

to figure out the implemented scoring logic. The package uses three steps for targets selection. Namely: - sequence complementarity using a position-weighted local alignment algorithm - free energies of RNA-RNA duplexes...functions to the purpose of understanding the package scoring criteria. After all, it looks like a sequence alignment problem ... Thank you, Maura -----Messaggio originale----…

miRNA Alignment biomaRt miRNA Alignment biomaRt

updated 16.4 years ago • mauede@alice.it

I have used DESeq2 for differential gene expression analysis and found discrepancies of gene ranking from two pipelines upstream of DESeq2: STAR-rsem-tximport...STAR-salmon-tximport.. Some of the discrepancies are quite large and I picked one gene here that ranked No98 from rsem-tximport but No.3 from salmon-tximport. It turned out that both rsem and salmon gave the...same count numbers but they …

deseq2 tximport rsem saimon

updated 7.7 years ago • LD

<div class="preformatted"> Dear All, I hope it is OK to send a general request for images to the bioconductor mailing list. Nature journal is about to publish a Feature on the statistical analysis of DNA microarray experiments. The Bioconductor Project is mentioned in the article. I am looking for pictures to illustrate the text and am hoping that you might be able to provide me with ima…

Microarray Microarray

updated 22.5 years ago • Loriot, Sarah

Hi, I am interested in comparing the expression of genes within the same sample and ranked them from the most expressed to the least expressed. I cannot use counts nor normalized...counts because they do not take into account the gene lengths. Which measure would you suggest I use? Does DESeq2 provides a function to transform raw counts into such format

gene expression rnaseq deseq2

updated 7.0 years ago • chiara.facciotto

I have two granges objects that I want to overlap based on the metadata column gene names - I essentially want to find the ranges that correlate to the same gene names between the two sets. Can anyone help

GenomicRanges

updated 4.5 years ago • grr4006

The codes and instructions for annotating gene names to the result table for differential gene expression analysis in DESeq2 seem to be for using Ensembl as the reference...genome in the alignment step. I'm wondering if there are instructions/codes for annotating gene names if I used UCSC hg19 as the reference genome in the alignment step? Thanks for your help

deseq2 gene names differential gene expression

updated 10.8 years ago • anpham

Hi, I am doing a differential expression analysis of small RNA using edgeR. I have 4 normal and 4 diseased samples, all samples are paired. Now, I have very little knowledge of statistics so I would appreciate clarification on the following: When I do the analysis without any per-filtering of low abundant genes, I get, let's say about 10-12 values in the FDR column with FDR < 0.05.…

edgeR FDR p-value Benjamini-Hochberg Differential Analysis

updated 6.9 years ago • ilovesuperheroes1993

regions and quantify these separately from all other reads (background reads). I'm then doing a gene-based DGE analysis, but am wondering whether this analysis might be affected by differences in isoform usage between...What if one treatment group uses longer isoforms than the other group? In standard DGE, transcript length matters because longer transcripts produce more reads, but I can't quite …

Transcriptomics DESeq2

updated 3.5 years ago • marius.wenzel

estimate the DE analysis and it went well. Now I use CPM normalized files to explore some specific genes expression in multiple pathways. I am aware that CPM are corrected for library size without considering gene length...RPKM normalized file. But even after reading similar posts, I am not sure how can I get input gene length to rpkm() function. This [discussion][1] tells that recent version of …

Normalization edgeR RPKM

updated 5.2 years ago • anikng

two the tximport object (untreated vs treated) from salmon,which is a S4 object has four cols name as abundance, counts, length, and countsfromabundance.My question is how to merge these two dataset into one so I could

deseq2 tximport

updated 6.5 years ago • rensanhao

Hi,   I would like to compare aligned reads back to the reference sequence. Matches, mismatches, insertions and deletions are present in my alignments but no soft/hard clipping. I aim for having...occurring (mis)matches\\indels per position (of the read) over all reads. I get the position and length of indels by means of explodeCigarOps and explodeCigarOpLengths. I also know how…

bam indel genomicalignments biostrings

updated 11.2 years ago • Stefanie Tauber

learnt that BioMart can extract a lot of data from Ensembl (from where I have been told to get the genes info) and can also download the validated miRNAs compressed files. I stress the main problem I am experienciing, though...is still open. In fact I have to find a piece of data that allows me to relate all the gene info I can get from BioMart querying Ensembl to the downloaded miRNAs info. Thi…

miRNA Biophysics Biostrings biomaRt miRNA Biophysics Biostrings biomaRt

updated 16.6 years ago • mauede@alice.it

3 treatments, I have created a heatmap with the geneIDs but I am struggling to find a way to add gene names or alternatively produce a list of gene names that are deferentially expressed. I have a GFF3 file and a cds file

DESeq2

updated 2.9 years ago • Chelsea

csv) in a bioinformatic context. I wonder, if there is a convention on how the "features" are named for DESeq2 csv outputs. In one of my sample datasets for genes for example, genes are named with "geneName.gene". Would an...example for CDS be named "cdsName.cds"? Is the .gene an error and the name column would normally contain only the feature name? Thanks in advance

deseq2 gene format

updated 6.5 years ago • miriam.mueller

file gencode.v28.long\_noncoding\_RNAs.gtf. To compute TPM and FPKM from the counts I first need the lengths of the lncRNA genes, which I obtain by summing their exon lengths accounting for overlaps using the R package GenomicFeatures...Then I compute effective length as gene length minus average fragment length + 1 (average fragment length was average insert length for any sample as...provided t…

GenomicFeatures TPM FPKM lncRNA

updated 7.6 years ago • Ina Hoeschele

solve..) My question here is: can you recommend options for analysis I can look into to get the most out of long-read sequencing? For example isoformswitchanalzer. This is the first time long read sequencing is done on...these organs in this disease so I don't have a particular question, I have been told that short-read sequencing is probably better if you are just looking at gene expression b…

DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq

updated 21 months ago • 09191919

Hello All, I am trying to load E. coli genes from a gff3 with makeTranscriptDbFromGff but am getting the following error: > chrominfo <- data.frame(chrom=c('ecoli...found In addition: Warning message: In if (is.na(chrominfo)) { :   the condition has length > 1 and only the first element will be used I have seen posts from others with similar issues but ha…

genomicfeatures rnaseq

updated 11.1 years ago • agd27

div class="preformatted">Hello, You can estimate the fragment length through strand cross-correlation analysis. The MACS peak caller will give you an estimate of fragment length based...on this (or possibly a similar method; I don't remember the precise method used). Most peak callers also allow you to specify the fragment length explicitly. The fragment length (or estimated fragment length..…

updated 12.0 years ago • Ryan C. Thompson

Hi, I'm running into an error when trying to extract sequences from fasta files using Rsamtools. I have a fasta file and a GRanges object, and I'd like to extract the sequences corresponding...ranges from the fasta file. When using the fasta file for the whole genome, scanFa throws an error. Sequences up to chr 5: 32500021 can be retrieved, but trying to retrieve any sequence after chr 5…

Rsamtools

updated 5.2 years ago • jlee

the case on at least two of the GO nodes in the list of significant over-represented GO terms: > length(geneIdsByCategory(test)[["GO:0051179"]]) [1] 89 > geneCounts(test)["GO:0051179"] GO:0051179 20 > length(geneIdsByCategory(test...probe sets from the chip used in the particular study. i was wondering, if u reduce the set of genes from the gene universe (n.GU)…

GO rat2302 probe GOstats topGO GO rat2302 probe GOstats topGO

updated 18.7 years ago • Jesper Ryge

Hello, I have some gene expression data for different tissue types with multiple replicates. My species has undergone a historical duplication...I am looking to compare the genome copies to identify which one is more highly expressed. Due to the nature of the count data, most parametric models don't seem to be a good fit for my problem. I was looking into the `voom` paper and...voom` transformed…

stats r RNASeqData limma voom

updated 2.2 years ago • pl23

I would like to run gene set variance analysis (GSVA) on RNA sequencing data using the `` GSVA `` package, but I am confused as to what kind of input...data for GSVA. What is the appropriate type of input for using the `` gsva() `` function on RNA sequencing data? If this is raw read counts, then what is the exact pre-processing performed 'under the hood'? If this is normalized...data, i…

rnaseq rna-seq preprocessing gsva

updated 9.4 years ago • t.kuilman

869 estimated genes. When I use affy and use the function ReadAffy() and rma I get an expression set with 32321 features. Very different from...chip. Please help me to open my eyes or enlighten me (and many others)!] However, when I want to get gene Symbols corresponding to the transcripts, again there is a number mismatch. For example when I used the package 'hugene10sttranscriptcluster.…

Microarray Annotation PROcess xps Microarray Annotation PROcess xps

updated 14.0 years ago • Azby Cdex

You may want to have a look at the Bioconductor package OrderedList. It searches for similarities in gene rankings without forcing the user to specify a threshold, where to cut the lists. Hope this helps, Cheers, Claudio -----Original...Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> Subject: [BioC] similarity between two gene lists with varied length Dear listers, a little o…

OrderedList OrderedList

updated 17.4 years ago • Claudio Lottaz

I would like to use UniProt.ws to convert UniProt ids to SGD ids for Saccharomyces cerevisiae but my attempts so far have resulted in the error: Error in .select(x, keys...where I attempt to convert "I2HB52". The expected answer is "YBR056W-A" (see http://www.uniprot.org/uniprot/I2HB52 ). <pre> library(UniProt.ws) taxId(UniProt.ws) <- 4932 species(UniProt.ws) res &…

uniprot.ws uniprot ensembl

updated 11.0 years ago • Joseph Barry

and I don't have a high quality genome assembly to go with it. I have carried out transcript-level abundance pseudoalignments with salmon, and I'd like to get gene-level abundances, but I'm not quite sure how to do this. It seems...used to get this, but from all of the examples I've seen, it seems that it requires a known set of genes, presumably from a sequenced genome project. Is it possible t…

tximport salmon rna seq de novo

updated 7.3 years ago • RMRG

is used in the library-size normalization of the SPRING tool (only genes making up <5% of total counts in every cell are used for normalization): https://github.com/AllonKleinLab/SPRING/blob...This type of exclusion might help with datasets where some cell types have a few dominant genes making up most of the counts, like secretory cells such as pancreatic beta cells or Paneth cells of …

single-cell RNA-seq scran normalization

updated 6.4 years ago • daniel.borshagovski

I'm wondering is that possible to find if the sequence is enriched by specific motifs? For example, I have generated Granges object and DNAStringset : ```r > gr_up <- GRanges...chrX 136548590-136549007 + | ENSG00000102243 0.0559441 0.100380 ------- seqinfo: 23 sequences from an unspecified genome; no seqlengths > seqs_up <- getSeq(BSgenome.Hsapiens.UCSC.h…

MotifDiscovery RNASeq

updated 3.8 years ago • Liliian

a very large and open question concerning the methods to analyse genome editing experiments with sequencing. I am using the CRISPR system to create indels at precise locations in the genome and I am interesting to determine...the efficiency of gene disruption by determining the percentage of reads containing indels. I am planning to amplify by PCR the target region...and then to use paired-end se…

indel sequencing alignment

updated 10.7 years ago • Merienne Nicolas

I would like to find the protein sequence for human APOB. I was not able to query by "APOB" so I first looked up the Entrez ID, 338. ``` library(UniProt.ws) human <- UniProt.ws...9606) keys <- c("338") columns <- c("SEQUENCE","UNIPROTKB","PDB") kt <- "ENTREZ_GENE" res <- select(human, keys, columns, kt) ``` This returns the main protein, but also…

Uniprot Annotation Identifiers

updated 6.7 years ago • Juliet Hannah

nbsp;  $ ./dmtcp\_restart\_script.sh As the BioConductor community is one of the most diverse and largest users of R, we would like to get an idea if people would find these features helpful.  We would be...nbsp; http://dmtcp.sourceforge.net/contactUs.html We look forward to your comments. Best wishes, - Gene Cooperman

dmtcp

updated 10.0 years ago • gene

7) res <- nbinomTest( cds, "N", "T" ) I get numbers under ids because on page 4 we removed the gene names. countsTable <- countsTable[ , -1 ] How can i get my res to match what is in the manual with gene names under id? Thanks, Mary

DESeq DESeq

updated 14.1 years ago • Mary Ann Allen

function estimateGLMTagwiseDisp to look at dispersion estimates for my data. When I plotted tags vs abundance, I see a strange shape (data artifact ). Would you please help me understand what property of the data can cause this...gt; plot(y$abundance,y$tagwise.dispersion) https://docs.google.com/file/d/0B_mk9qnFziV- ZFBhak5fUGZSZ09VV0dJQ21Id1hYQQ/edit Thanks

updated 13.9 years ago • Alpesh Querer

I have a collection samples spanning 3 different studies. I am performing differential abundance to identify the OTUs which are significant in seawater vs membranes. With the entire collection, I can easily do...x Membrane -y Seawater -d   I also want to perform differential abundance for each study individually. Can I just add a new column into my mapping file called `` SourceStudy…

deseq2 qiime

updated 8.3 years ago • syafiqkamarulazman

refgff3, format = "gff3", circ_seqs = character()) #or gtf ebg <- exonsBy(txdb, by="gene") bamfile <- BamFile(readsBAM) se <- summarizeOverlaps(features=ebg, reads=bamfile, mode="Union", singleEnd=FALSE,ignore.strand...__ <pre> Error in .normargSeqlevels(seqnames) : supplied 'seqlevels' cannot contain duplicated sequence names</pre> --- It's …

software error

updated 7.9 years ago • c.legrand

corresponding to the entire genes, or to their flanking sequences, or to some upstream sequences, or to the last 10 or 20 nucleotides of each genes. Each genomic...range is defined by a sequence name (e.g. chr1), a start position, an end position, and a strand. Here is an example of how to extract the last 10 nucleotides...gn)) # check length of shortest gene gn_last10 <- flank(gn, -1…

Cancer BSgenome BSgenome IRanges Cancer BSgenome BSgenome IRanges

updated 11.4 years ago • Hervé Pagès

Dear all, `` txImport `` requires a txdb file with correspondences between transcript names and gene names. In the sample data provided by `` txImportData ``, there is a pre-constructed table. I was interested in reconstructing...it from the sequence files, but I ended up with a discrepancy: a gene (3 transcripts) seem to be present in the files, but not the table (see code...reasoning? Is it s…

txImportData txImport

updated 5.0 years ago • alexlok

Hi everyone, I'm trying to use CHIPseeker for CutnTag data, and had a question regarding getting the names of each annotation. I've used annotatePeak to get an idea about the promoter, exon and intergenic region, but is there a...everyone, I'm trying to use CHIPseeker for CutnTag data, and had a question regarding getting the names of each annotation. I've used annotatePeak to get an idea a…

ChIPseeker CHIPsee

updated 4.6 years ago • rithika.behera

I am the author of KEGGprofile package. Thanks for using my package. I think defining the reference genes based on your own experiments is the most reasonable method for finding overrepresentation pathways. For example...the high abundance proteins were easier to be identified in a proteomics experiment because of the limitation of current analysis...to find the overrepresented pathways for signi…

Proteomics Pathways KEGGprofile Proteomics Pathways KEGGprofile

updated 13.0 years ago • slzhao

and the _BSgenome.Hsapiens.UCSC.hg19_ _R/Bioconductor_ packages, I generate DNA sequences of 200bp length centered on the probes being processed and save them as FASTA files. Afterwards, I feed them to MEME...for the results. Some motifs were appearing for every subset we were testing. Specifically, the most common motifs were repetitive sequences of the same nucleotide (polyA, polyC, polyG, pol…

illumina 450k motifs meme

updated 10.0 years ago • Gustavo Fernández Bayón

are missing their RNA ends and almost as many are missing either a 5' UTR or a 3' UTR. /nb/dario/genes$ egrep -c "(HAVANA|ENSEMBL) transcript" gencode.v17.annotation.gtf 194871 /nb/dario/genes$ egrep "(HAVANA|ENSEMBL) transcript...gencode.v17.annotation.gtf | grep -c mRNA_end_NF - 21699 /nb/dario/genes$ egrep "(HAVANA|ENSEMBL) transcript" gencode.v17.annotation.gtf | grep -c cd…

Transcription Annotation Transcription Annotation

updated 12.4 years ago • Dario Strbenac

<div class="preformatted">Tophat2 cmd: tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensem bl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome 001.fastq.gz Cufflinks cmd: cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotati…

updated 11.9 years ago • Sindre

Preprocessing and DE analysis using affy and limma packages But now, I am starting to work with Gene ST array and I will soon have to work with Raw data from HTA array. So I tried to convert myself to the oligo package, however...the documentation for this package is directed to the HGU95, and it is not easily adaptable to the Gene ST for a neophyte like me. So my question for you is : Do you …

oligo hugene20st

updated 9.6 years ago • giroudpaul

Hello. I am trying to calculate per cell TPMS for all the genes in my single-cell dataset in order to find cells that might ectopically express genes that are nto supposed to be there...So far, I found the gene lengths and have divided my count matrix by the gene lengths to get the rpk. My plan is to read the rpk back into the sce object...assay( <singlecellexperiment>, i="characte…

SingleCellExperiment

updated 24 months ago • JalapenoCornbread