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26
votes
16
replies
26k
views
Differential expression analysis starting from TPM data
R TPM
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 60
22
votes
14
replies
1.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 22 days ago by • 0 • written 6 weeks ago by ▴ 50
18
votes
6
replies
24k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 8 weeks ago by • 0 • written 5.4 years ago by ▴ 50
14
votes
13
replies
22k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ▴ 20
10
votes
8
replies
1.3k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
2.9 years ago m93 ▴ 10
10
votes
13
replies
3.2k
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 6.9 years ago by • 0 • written 6.9 years ago by ▴ 10
9
votes
6
replies
1.8k
views
Any method can coerce "list" object to GRanges [reproducible example is included]?
granges error handling R
updated 6.2 years ago by 11k • written 6.2 years ago by ▴ 70
9
votes
7
replies
2.6k
views
WGCNA: relate modules to binary trait
WGCNA module eigengene binary trait R
updated 3.4 years ago by ▴ 30 • written 3.4 years ago by ▴ 50
8
votes
11
replies
950
views
Creating design matrix in LIMMA
limma microarray R
5.4 years ago sgblackpearl • 0
8
votes
9
replies
5.1k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 6.9 years ago by • 0 • written 6.9 years ago by ★ 1.5k
8
votes
5
replies
1.6k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 3.1 years ago by 45k • written 3.1 years ago by ▴ 90
8
votes
4
replies
634
views
maintainer option for bioconductor packages
bioconductor R
updated 3.6 years ago by 60k • written 3.6 years ago by ▴ 70
7
votes
8
replies
839
views
Where downloaded data are stored?
R
7.1 years ago Arman Shahrisa ▴ 20
7
votes
1
reply
993
views
What is the best way to get help on Bioconductor packages?
Bioconductor R Suggestion
updated 6.9 years ago by ★ 8.2k • written 6.9 years ago by ▴ 10
7
votes
13
replies
2.1k
views
Finding the coordinates from a BCV plot in edgeR
r edgeR estimatedispersions coordinate
6.5 years ago pertille • 0
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
5.5 years ago Jon Bråte ▴ 190
7
votes
15
replies
1.4k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 3.9 years ago by 45k • written 3.9 years ago by ▴ 50
7
votes
8
replies
17k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 7.3 years ago by ▴ 600 • written 7.3 years ago by ▴ 20
7
votes
5
replies
910
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
18 months ago ecg1g15 • 0
7
votes
9
replies
1.1k
views
codelink package is not installing
codelink r
7.1 years ago Agaz Hussain Wani ▴ 260
7
votes
13
replies
1.0k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 2.2 years ago by ★ 2.9k • written 2.2 years ago by ▴ 90
7
votes
7
replies
866
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 40
7
votes
10
replies
6.8k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 4.9 years ago by 13k • written 4.9 years ago by • 0
6
votes
4
replies
2.1k
views
deseq2 estimating size factors
r deseq2
updated 6.1 years ago by 37k • written 6.1 years ago by ▴ 40
6
votes
3
replies
1.5k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 10
6
votes
7
replies
2.7k
views
unexpected error when creating GRanges object by calling makeGRangesFromDataFrame()
r error handling granges
updated 6.3 years ago by 15k • written 6.3 years ago by ▴ 70
6
votes
3
replies
2.0k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 3.2 years ago by 13k • written 3.2 years ago by ▴ 60
6
votes
3
replies
6.2k
views
Heatmap Plotting in R
heatmap R bioconductor
6.9 years ago • updated 5.2 years ago Deepak Tanwar ▴ 10
6
votes
7
replies
1.1k
views
How to implement element-wise-overlaps with iteration for two different bed files in R?
r findoverlaps iterators
updated 6.4 years ago by 15k • written 6.4 years ago by ▴ 70
6
votes
7
replies
1.5k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 3.1 years ago by ★ 2.6k • written 3.1 years ago by ▴ 10
6
votes
7
replies
1.4k
views
Differences between RTCGA and TCGAbiolinks data
r survival analysis rtcga tcgabiolinks mirna-seq
4.0 years ago atakanekiz ▴ 30
6
votes
2
replies
1.2k
views
permutation test against intervals
R pkg
updated 7.0 years ago by ▴ 30 • written 7.2 years ago by ▴ 20
6
votes
6
replies
1.2k
views
Can i set a path for readCodlinkSet()
r differential expression codelink
updated 6.9 years ago by ▴ 760 • written 7.0 years ago by ▴ 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 7.3 years ago by 45k • written 7.3 years ago by ▴ 780
6
votes
11
replies
5.3k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 5 months ago by ▴ 30 • written 6.3 years ago by ▴ 70
5
votes
2
replies
873
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
5.9 years ago • updated 5.5 years ago Jurat Shahidin ▴ 70
5
votes
11
replies
1.8k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
3.0 years ago • updated 2.9 years ago pierre.marin • 0
5
votes
3
replies
793
views
How to avoid repeated overlap pair for GRanges object in grid?
r genomicranges
5.8 years ago • updated 5.5 years ago Jurat Shahidin ▴ 70
5
votes
0
replies
925
views
Job: Summer Studentships in Data Science (Computational Cancer Biology) at the University of Cambridge
R python deep learning machine learning cancer genomics Job
5.2 years ago • updated 5.1 years ago Shamith.Samarajiwa ▴ 180
5
votes
3
replies
2.3k
views
Please use the function 'listAttributes' to get valid attribute names
r biomart
4.9 years ago al14 • 0
5
votes
4
replies
2.8k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
5.1 years ago • updated 4.9 years ago salamandra ▴ 20
5
votes
10
replies
1.0k
views
caught segfault error when loading S4Vectors package in R
R S4Vectors segfault
updated 3.3 years ago by 25k • written 3.3 years ago by • 0
5
votes
14
replies
2.8k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 27 days ago by ★ 1.2k • written 3.9 years ago by ▴ 50
5
votes
22
replies
4.3k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 5.9 years ago by ▴ 990 • written 7.3 years ago by • 0
5
votes
1
reply
1.5k
views
finding overlapping regions within 2 different bed files with different features
R annotation
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 50
5
votes
1
reply
1.4k
views
WGCNA - looking for over-representation of DEGs within gene networks
wgcna r differential gene expression bioconductor
updated 6.4 years ago by ★ 2.6k • written 6.4 years ago by ▴ 30
5
votes
7
replies
817
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 4.4 years ago by ▴ 150 • written 4.4 years ago by • 0
5
votes
3
replies
1.1k
views
Only 1s created by erode()
r ebimage morphology
updated 5.8 years ago by ▴ 750 • written 5.8 years ago by • 0
5
votes
5
replies
809
views
How to extract out wanted IntegerList more elegantly from nested list?
r s4vectors integerlist iranges
updated 5.7 years ago by 11k • written 5.7 years ago by • 0
5
votes
9
replies
2.5k
views
Fitted values from EdgeR
edger r
6.9 years ago R ▴ 40
50 results • Page 1 of 1
Recent ...
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Comment: Italicise by Kevin Blighe 3.5k
Okay, I am guessing that the problem is that you need to update the version of *EnhancedVolcano* to the latest version. Can you try that? T…
Comment: Italicise by Pau • 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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