Showing : r • reset
2
votes
27
replies
2.3k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek sgrna crispr cas9 R
6.9 years ago • updated 6.8 years ago alexgraehl ▴ 20
3
votes
26
replies
3.0k
views
How to prepare targets.txt file in codelink.
r codelink
updated 7.3 years ago by ▴ 760 • written 7.3 years ago by ▴ 260
2
votes
23
replies
2.2k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 5.9 years ago by 37k • written 5.9 years ago by • 0
5
votes
22
replies
4.3k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 6.1 years ago by ▴ 990 • written 7.5 years ago by • 0
1
vote
22
replies
3.0k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 5.6 years ago by ▴ 10 • written 6.0 years ago by • 0
0
votes
19
replies
1.1k
views
Paired Difference Analysis
deseq2 R differential gene expression
5.0 years ago • updated 4.9 years ago nhua • 0
1
vote
19
replies
15k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 4.3 years ago by 46k • written 4.3 years ago by ▴ 10
1
vote
18
replies
2.4k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
4.4 years ago stephan.emmrich • 0
3
votes
18
replies
2.0k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 7.3 years ago by ▴ 760 • written 7.3 years ago by ▴ 260
4
votes
17
replies
1.5k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma r differential gene expression
updated 5.1 years ago by 46k • written 5.1 years ago by ▴ 90
3
votes
16
replies
1.9k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 9 months ago by ▴ 10 • written 23 months ago by ▴ 10
3
votes
16
replies
2.5k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 70
26
votes
16
replies
27k
views
Differential expression analysis starting from TPM data
R TPM
updated 5.0 years ago by 46k • written 5.0 years ago by ▴ 60
0
votes
15
replies
1.3k
views
Is the STRINGdb server down?
STRINGdb R protein
updated 3.2 years ago by • 0 • written 3.4 years ago by • 0
7
votes
15
replies
1.5k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 4.2 years ago by 46k • written 4.2 years ago by ▴ 50
5
votes
14
replies
3.5k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 6.7 years ago by ★ 8.2k • written 6.7 years ago by ▴ 50
0
votes
14
replies
2.2k
views
Error in ReactomePA
r reactomepa
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by ▴ 20
5
votes
14
replies
2.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3 months ago by ★ 1.4k • written 4.1 years ago by ▴ 50
22
votes
14
replies
2.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 3 months ago by • 0 • written 4 months ago by ▴ 50
14
votes
14
replies
23k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 7 weeks ago by • 0 • written 5.1 years ago by ▴ 20
0
votes
14
replies
1.4k
views
Path to file in windows
bioconductor R windows diffbind
updated 5.3 years ago by ▴ 640 • written 5.3 years ago by • 0
4
votes
14
replies
7.7k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
7.1 years ago nickp60 • 0
1
vote
13
replies
1.4k
views
Why Differential expression results differ with edgeR and limma ?
limma edgeR differential gene expression r
5.0 years ago Biologist ▴ 90
7
votes
13
replies
1.2k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 2.4 years ago by ★ 2.9k • written 2.4 years ago by ▴ 90
7
votes
13
replies
2.2k
views
Finding the coordinates from a BCV plot in edgeR
r edgeR estimatedispersions coordinate
6.7 years ago pertille • 0
2
votes
13
replies
4.9k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 5.0 years ago by ▴ 20 • written 5.0 years ago by ▴ 90
2
votes
13
replies
1.8k
views
problems filtering antigenomic probes from HTA 2.0
pd.hta.2.0 R
6.0 years ago • updated 5.5 years ago s.munster ▴ 40
7
votes
13
replies
1.3k
views
Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
5.8 years ago Jon Bråte ▴ 190
10
votes
13
replies
3.3k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 7.1 years ago by • 0 • written 7.1 years ago by ▴ 10
1
vote
12
replies
1.5k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r iranges findoverlaps IntegerList List
6.0 years ago • updated 5.8 years ago jian_liangli • 0
1
vote
12
replies
561
views
Taking much longer time for same script after R upgrade to 4.0
R
2.2 years ago hsiowa2 ▴ 20
4
votes
12
replies
4.1k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 4.3 years ago by 46k • written 4.3 years ago by ▴ 90
0
votes
12
replies
1.2k
views
DESeq2 different versions
rnaseq r deseq2
updated 4.8 years ago by 37k • written 4.8 years ago by • 0
0
votes
11
replies
2.6k
views
Remove NaN from a list or replace NaN with a value.
R meta-analysis
updated 12 months ago by • 0 • written 3.8 years ago by ▴ 10
8
votes
11
replies
1000
views
Creating design matrix in LIMMA
limma microarray R
5.6 years ago sgblackpearl • 0
6
votes
11
replies
5.5k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 8 months ago by ▴ 40 • written 6.5 years ago by ▴ 70
0
votes
11
replies
602
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData r
3 months ago Mohamed • 0
5
votes
11
replies
1.9k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
3.2 years ago • updated 3.1 years ago pierre.marin • 0
5
votes
11
replies
833
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 2.0 years ago by ★ 5.7k • written 2.0 years ago by • 0
2
votes
10
replies
1.4k
views
DiffBind consensus peak help
diffbind r chipseq
updated 4.9 years ago by ★ 4.4k • written 5.0 years ago by • 0
4
votes
10
replies
1.1k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 3.6 years ago by 37k • written 3.6 years ago by • 0
2
votes
10
replies
919
views
Am I on the right tracks with a 3 factor design in Limma?
r limma design matrix biobase
updated 4.1 years ago by 46k • written 4.1 years ago by • 0
7
votes
10
replies
7.3k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 5.1 years ago by 13k • written 5.2 years ago by • 0
5
votes
10
replies
1.1k
views
caught segfault error when loading S4Vectors package in R
R S4Vectors segfault
updated 3.5 years ago by 25k • written 3.5 years ago by • 0
4
votes
10
replies
7.5k
views
How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R?
R bioconductor granges
6.5 years ago • updated 6.1 years ago pertille • 0
2
votes
10
replies
18k
views
Heatmap with error message: `x' must be a numeric matrix
r heatmap numericmatrix
updated 6.4 years ago by ★ 1.5k • written 6.4 years ago by ▴ 90
0
votes
10
replies
1.3k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error RNAseq tximport R
updated 3.0 years ago by 37k • written 3.0 years ago by • 0
0
votes
10
replies
1.1k
views
How to get feature ID's from the raw codelink data.
r codelink
7.3 years ago Agaz Hussain Wani ▴ 260
6
votes
10
replies
3.9k
views
defining a function for multiple paired t.test in many rows of a microarray dataset
microarray r t.test bioconductor
updated 7.6 years ago by 46k • written 7.6 years ago by ▴ 800
2
votes
10
replies
6.3k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 5.9 years ago by 37k • written 5.9 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: How to retrieve Entrez IDs using Gene Symbols? by Basti ▴ 390
Cross-posted : https://www.biostars.org/p/9535046/#9535054
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
It's relevant for me, thank you for the information!
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
Thank you for sharing!
Comment: conditional command within GRanges by Basti ▴ 390
I can't reproduce your issue because you did not provided an example of your dataset (example with `dput(head(data1))`, but in the first ca…
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
That sounds like you have the wrong version of the annotation compared to which version you used for the quantification?
Votes
Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
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