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3
votes
24
replies
3.3k
views
Problem in installing maEndToEnd package
microarray
maEndToEnd
4.7 years ago • updated 4.6 years ago
Jack
• 0
0
votes
24
replies
3.2k
views
SomaticSignatures
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
Guest User
★ 13k
1
vote
24
replies
4.8k
views
GenomicAlignments - extracting sequence signatures from bam file
bam file
HIV
cytosine
6.6 years ago • updated 6.5 years ago
achaillon
• 0
8
votes
24
replies
3.5k
views
GenomicFeatures: Select exons by transcript. Any faster option than exonsBy?
GenomicFeatures
updated 8.1 years ago by
Martin Morgan
25k • written 8.1 years ago by
stianlagstad
▴ 90
11
votes
23
replies
2.6k
views
crlmm support for Illumina arrays with no annotation package?
crlmm
QCarray
annotation
updated 4.3 years ago by
milo.yanez20
• 0 • written 4.5 years ago by
deanpett
▴ 30
5
votes
23
replies
6.2k
views
Convertion of indexed bam file to tsv file format
python
samtools
updated 8.5 years ago by
Hervé Pagès
16k • written 8.5 years ago by
malikbashirkhan2
• 0
1
vote
23
replies
2.4k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
Lna
• 0
2
votes
23
replies
3.5k
views
Coping with a label/class imbalance in DESeq2
deseq2
rnaseq
r
regression
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
bkellman
• 0
1
vote
23
replies
2.4k
views
Sample label swap in HTML results
dexseq
dexseqhtml
updated 6.8 years ago by
Alejandro Reyes
★ 1.9k • written 6.8 years ago by
maximinio
• 0
0
votes
23
replies
2.6k
views
VariantAnnotation geno function
variantannotation
7.5 years ago
ribioinfo
▴ 100
3
votes
23
replies
3.8k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery
VROOM
2.4 years ago
array chip
▴ 420
10
votes
23
replies
13k
views
Macbook M1 install genefilter failed
DESeq2
m1
macbook
genefilter
2.7 years ago • updated 17 months ago
soda
▴ 80
8
votes
23
replies
847
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 13 days ago by
Robert Castelo
★ 3.3k • written 14 days ago by
Bine
▴ 40
1
vote
22
replies
5.1k
views
DESeq2 for Ribosomal profiling analysis
deseq2
8.1 years ago
jxu006
▴ 10
2
votes
22
replies
4.2k
views
Error in 'colnames' while running case 1 of TCGABiolinks
tcgabiolinks
Error in `colnames
8.2 years ago
zeeniajagga
• 0
1
vote
22
replies
4.6k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 7.3 years ago by
theobroma22
▴ 10 • written 7.7 years ago by
wssdandan2009
• 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago
Chris
• 0
0
votes
22
replies
3.0k
views
'x' has "out of limits" views ,Issue with the file size!! Compareequence function is not working
compilation error
filesize
bioconductor
6.7 years ago
susobhanbaidya
• 0
6
votes
22
replies
3.9k
views
Oligo package: paCalls questions
microarray
oligo
updated 8.9 years ago by
cstrato
★ 3.9k • written 8.9 years ago by
whyuen
▴ 20
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 8 weeks ago by
Michael Love
41k • written 7.8 years ago by
adesrichard
▴ 30
1
vote
22
replies
4.8k
views
DESEq2 Large Memory When Parallel
deseq2
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
Jeff Granja
▴ 10
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
26
votes
22
replies
18k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 6.8 years ago by
k.vitting.seerup
▴ 120 • written 8.6 years ago by
tangming2005
▴ 190
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 4 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
3
votes
21
replies
2.8k
views
`precede` does not perform as expected
genomicranges
precede
ph525.5x
7.3 years ago
wcstcyx
▴ 30
1
vote
21
replies
5.1k
views
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0
BiocManager
written 3.9 years ago by
Lucy
▴ 60
9
votes
21
replies
11k
views
annotate GRanges with upstream or downstream nearest gene
GRange
genomicranges
genomicfeatures
updated 8.3 years ago by
Ou, Jianhong
★ 1.3k • written 8.3 years ago by
tangming2005
▴ 190
9
votes
21
replies
5.3k
views
limma - complex design with paired samples, sex and batch effect
limma
paired samples
complex-design
8.3 years ago
aec
▴ 90
4
votes
21
replies
3.4k
views
RMA normaliztion using XPS
normalization
xps
updated 9.0 years ago by
cstrato
★ 3.9k • written 9.0 years ago by
dhwani.dholakia
• 0
0
votes
21
replies
4.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
8.9 years ago
pifferdavide
• 0
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Xiao
• 0 • written 9.2 years ago by
aristotele_m
▴ 40
14
votes
21
replies
11k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation
shortread
dependency
updated 4.9 years ago by
January Weiner
▴ 240 • written 6.0 years ago by
joseph.elsherbini
▴ 60
4
votes
21
replies
11k
views
DESeq2 and ComBat
deseq2
combat
updated 8.3 years ago by
Bernd Klaus
▴ 610 • written 8.3 years ago by
ribioinfo
▴ 100
9
votes
21
replies
15k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
updated 21 months ago by
SmallChess
▴ 10 • written 3.5 years ago by
georgia.katsoula
▴ 40
7
votes
21
replies
3.4k
views
ANOVA using edgeR
edger
8.2 years ago
myprogramming2016
• 0
34
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.6 years ago • updated 19 months ago
Michael Love
41k
0
votes
21
replies
5.1k
views
unable to readImage using EBImage package
EBImage
EBImage
updated 12.1 years ago by
Nurdiyanah Jambari
▴ 90 • written 12.2 years ago by
Guest User
★ 13k
0
votes
21
replies
2.8k
views
How to use DECIPHER to design group-specific primers
Decipher
4.0 years ago
hoonhuiyi
• 0
0
votes
21
replies
3.3k
views
Heatmap problem
15.2 years ago
hemant ritturaj
▴ 150
13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.6 years ago
osa.zuta
▴ 40
1
vote
21
replies
3.4k
views
Rsubread stopping half-way through align
rsubread
7.8 years ago • updated 7.7 years ago
Campbell.1933
• 0
9
votes
21
replies
3.3k
views
Error when fitting linear model with technical replicates and blocking variable
limma
technical replicates
8.4 years ago
Eleni Christodoulou
▴ 150
11
votes
21
replies
5.0k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
Gary
▴ 20
0
votes
21
replies
3.2k
views
How to annotate genomic coordinates
convert
convert
11.5 years ago
José Luis Lavín
▴ 280
27
votes
21
replies
23k
views
Mapping genome regions to gene symbols
tcga cnv
gene symbol
coordinate
updated 17 months ago by
James W. MacDonald
65k • written 9.0 years ago by
NS
▴ 60
4
votes
20
replies
3.1k
views
TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid for atomic vectors
tcgabiolinks
updated 7.0 years ago by
Mike Smith
★ 6.5k • written 7.0 years ago by
tangming2005
▴ 190
9
votes
20
replies
2.7k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 9.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.1 years ago by
jessica.hekman
▴ 40
12
votes
20
replies
2.0k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma
multifactorial design
design and contrast matrix
affymetrix microarrays
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
svlachavas
▴ 830
0
votes
20
replies
2.3k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2
DEGs
2.8 years ago • updated 2.7 years ago
Ming
▴ 380
0
votes
20
replies
2.3k
views
VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
8.7 years ago • updated 8.5 years ago
Tjeerd Dijkstra
• 0
45,577 results • Page
2 of 912
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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