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r
•
reset
2
votes
27
replies
4.0k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek
sgrna
crispr
cas9
R
8.6 years ago • updated 8.5 years ago
alexgraehl
▴ 20
3
votes
26
replies
4.4k
views
How to prepare targets.txt file in codelink.
r
codelink
updated 9.1 years ago by
Diego Diez
▴ 760 • written 9.1 years ago by
Agaz Hussain Wani
▴ 260
2
votes
23
replies
3.6k
views
Coping with a label/class imbalance in DESeq2
deseq2
rnaseq
r
regression
updated 7.6 years ago by
Michael Love
42k • written 7.6 years ago by
bkellman
• 0
1
vote
22
replies
4.7k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 7.4 years ago by
theobroma22
▴ 10 • written 7.8 years ago by
wssdandan2009
• 0
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor
annotationforge
annotationdbi
annotation
r
updated 7.8 years ago by
Axel Klenk
★ 1.0k • written 9.2 years ago by
Stephen H
• 0
0
votes
19
replies
1.9k
views
Paired Difference Analysis
deseq2
R
differential gene expression
6.8 years ago • updated 6.7 years ago
nhua
• 0
1
vote
19
replies
25k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Merlin
▴ 10
3
votes
18
replies
2.8k
views
Annotating codelink data file
r
codelink
annotation
annotationdbi
updated 9.1 years ago by
Diego Diez
▴ 760 • written 9.1 years ago by
Agaz Hussain Wani
▴ 260
2
votes
18
replies
3.5k
views
Using tximport on rsem files produces error while trying to read in files
R
tximport
rnaseq
tpm
rsem
6.1 years ago
stephan.emmrich
▴ 10
4
votes
17
replies
2.7k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma
r
differential gene expression
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
Biologist
▴ 110
0
votes
17
replies
1.7k
views
How to check linear model
modalmatrix
limma
R
linear
15 months ago • updated 14 months ago
Jitendra
▴ 10
33
votes
16
replies
40k
views
Differential expression analysis starting from TPM data
R
TPM
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
cahidora
▴ 90
3
votes
16
replies
4.2k
views
Any way to proceed duplicate removal for list of GRanges object ?
r
grangeslist
duplicate
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
Jurat Shahidin
▴ 80
3
votes
16
replies
4.5k
views
How to add pseudocount to DESeq2 dds object
deseq2
r
updated 2.6 years ago by
Stanley
▴ 10 • written 3.7 years ago by
Jitendra
▴ 10
3
votes
16
replies
2.3k
views
Atena package - error (new user)
RNAseq
R
Atena
19 months ago • updated 15 months ago
lalanis1
• 0
7
votes
15
replies
4.3k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR
rnaseq
r
bioconductor
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Beginner
▴ 60
22
votes
15
replies
7.6k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 6 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
0
votes
15
replies
2.5k
views
Is the STRINGdb server down?
STRINGdb
R
protein
updated 5.0 years ago by
zhanghongjie000
• 0 • written 5.1 years ago by
shahroze786
• 0
5
votes
14
replies
4.8k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape
r
network
graphBAM object
updated 8.4 years ago by
Dan Tenenbaum
★ 8.2k • written 8.4 years ago by
alptaciroglu
▴ 50
0
votes
14
replies
3.4k
views
Error in ReactomePA
r
reactomepa
updated 7.9 years ago by
Guangchuang Yu
★ 1.2k • written 7.9 years ago by
Ram
▴ 20
5
votes
14
replies
5.0k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 2.0 years ago by
ATpoint
★ 4.1k • written 5.9 years ago by
Beginner
▴ 60
17
votes
14
replies
40k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 23 months ago by
OE
• 0 • written 6.8 years ago by
cms72
▴ 20
4
votes
14
replies
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.8 years ago
nickp60
• 0
2
votes
14
replies
7.6k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 15 months ago by
Chris
▴ 10 • written 6.8 years ago by
Biologist
▴ 110
0
votes
14
replies
2.3k
views
Path to file in windows
bioconductor
R
windows
diffbind
updated 7.0 years ago by
Gord Brown
▴ 650 • written 7.1 years ago by
jorrenkuster
• 0
7
votes
13
replies
2.3k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
7.5 years ago
Jon Bråte
▴ 250
1
vote
13
replies
2.3k
views
Why Differential expression results differ with edgeR and limma ?
limma
edgeR
differential gene expression
r
6.7 years ago
Biologist
▴ 110
2
votes
13
replies
3.2k
views
problems filtering antigenomic probes from HTA 2.0
pd.hta.2.0
R
7.8 years ago • updated 7.3 years ago
s.munster
▴ 40
7
votes
13
replies
2.6k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores
granges
phastCons100way.UCSC.hg38
r
rtracklayer
updated 4.2 years ago by
Robert Castelo
★ 3.3k • written 4.2 years ago by
Biologist
▴ 110
7
votes
13
replies
3.2k
views
Finding the coordinates from a BCV plot in edgeR
r
edgeR
estimatedispersions
coordinate
8.5 years ago
pertille
• 0
0
votes
13
replies
5.0k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
14 months ago
Laia
▴ 10
10
votes
13
replies
4.3k
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 8.9 years ago by
tree-ski
• 0 • written 8.9 years ago by
dennis.oezcelik
▴ 10
1
vote
12
replies
2.2k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r
iranges
findoverlaps
IntegerList
List
7.8 years ago • updated 7.5 years ago
jian_liangli
• 0
1
vote
12
replies
1.3k
views
Taking much longer time for same script after R upgrade to 4.0
R
3.9 years ago
hsiowa2
▴ 20
1
vote
12
replies
2.5k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 3 months ago by
Mary
• 0 • written 2.6 years ago by
Ming
▴ 380
5
votes
12
replies
6.6k
views
Filtering step for differential analysis in edgeR
r
edger
differential gene expression
filtering
bioconductor
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Biologist
▴ 110
0
votes
12
replies
1.8k
views
DESeq2 different versions
rnaseq
r
deseq2
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
minie
• 0
8
votes
11
replies
11k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5
r
hdf5
updated 12 months ago by
Yijing
• 0 • written 6.9 years ago by
him4u324
▴ 10
0
votes
11
replies
3.8k
views
Remove NaN from a list or replace NaN with a value.
R
meta-analysis
updated 2.8 years ago by
Tanya
• 0 • written 5.5 years ago by
morteza.hadizade
▴ 10
8
votes
11
replies
2.0k
views
Creating design matrix in LIMMA
limma
microarray
R
7.4 years ago
sgblackpearl
• 0
5
votes
11
replies
3.4k
views
DESeq2 logfoldchange and interaction in model
deseq2
R
logfoldchange
rna-seq
5.0 years ago • updated 4.8 years ago
pierre.marin
• 0
6
votes
11
replies
7.4k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges
split
r
updated 2.4 years ago by
jon.klonowski
▴ 40 • written 8.3 years ago by
Jurat Shahidin
▴ 80
6
votes
11
replies
1.8k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r
biomart
SNP
annotation
HUGO
updated 3.8 years ago by
Mike Smith
★ 6.5k • written 3.8 years ago by
aroso491
• 0
0
votes
11
replies
2.0k
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData
r
2.1 years ago • updated 2.0 years ago
Mohamed
▴ 30
2
votes
10
replies
2.1k
views
DiffBind consensus peak help
diffbind
r
chipseq
updated 6.7 years ago by
Rory Stark
★ 5.2k • written 6.7 years ago by
reubenmcgregor88
• 0
4
votes
10
replies
2.9k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
lkianmehr
• 0
4
votes
10
replies
9.2k
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
8.3 years ago • updated 7.9 years ago
pertille
• 0
2
votes
10
replies
1.8k
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
reubenmcgregor88
• 0
5
votes
10
replies
2.2k
views
caught segfault error when loading S4Vectors package in R
R
S4Vectors
segfault
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
ecg1g15
▴ 20
0
votes
10
replies
2.2k
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 4.8 years ago by
Michael Love
42k • written 4.8 years ago by
ScafioRuo
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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