0
votes
3
replies
3.5k
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 4.0 years ago by ▴ 780 • written 4.0 years ago by • 0
1
vote
4
replies
2.3k
views
Differential Splicing using edgeR
diffSpliceDGE edgeR DifferentialSplicing
4.0 years ago Assa Yeroslaviz ★ 1.5k
2
votes
1
reply
1.4k
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 180
1
vote
7
replies
2.3k
views
TSSEscore function in ATACseqQC package
ATACseqQC
4.0 years ago • updated 3.9 years ago Liu Yu-Yu • 0
0
votes
3
replies
2.8k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 4.0 years ago by 53k • written 4.0 years ago by ▴ 90
1
vote
3
replies
2.1k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.9 years ago by • 0 • written 4.0 years ago by • 0
1
vote
4
replies
2.6k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
2
votes
1
reply
2.7k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
votes
2
replies
1.6k
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db org.Sc pathview
4.0 years ago chase.mateusiak • 0
0
votes
2
replies
1.5k
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
4.0 years ago IamFrofro • 0
3
votes
6
replies
17k
views
Error: Faceting variables must have at least one value when plotting with ChIPQC
ChipQC chipqc
updated 3.3 years ago by • 0 • written 9.4 years ago by ▴ 10
0
votes
4
replies
1.6k
views
Large DE LogFC range
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 20
0
votes
1
reply
1.1k
views
DESeq2 Responder vs Non-Responders nested design
paired-samples DESeq2 interactionterm nested-design
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
5
replies
2.5k
views
Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
0
votes
1
reply
1.4k
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
vote
2
replies
1.6k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
4.1 years ago • updated 3.9 years ago A ▴ 60
0
votes
3
replies
1.4k
views
Error in loading data set
ExpressionData
updated 4.0 years ago by ▴ 780 • written 4.0 years ago by • 0
0
votes
2
replies
2.2k
views
A mistake came when I install some packages using "biocmanager"
biocmanager
4.0 years ago f1014063507 • 0
0
votes
0
replies
869
views
RNA seq of 4 groups p_values
R analysis p_values RNASeq
updated 4.0 years ago by 21k • written 4.0 years ago by • 0
0
votes
1
reply
3.8k
views
Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 3.5 years ago by • 0 • written 4.0 years ago by • 0
1
vote
1
reply
911
views
Problems to find the pvalues via rowttests
rowttests
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
0
votes
1
reply
1.0k
views
How to insert a qvalues column in a dataframe with pvalues in R
qvalues dataframe
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
0
votes
0
replies
1.3k
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
4.0 years ago zroger499 • 0
1
vote
2
replies
3.7k
views
airway package not compatible with R version 4.1.2 (2021-11-01)
airway
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by • 0
0
votes
1
reply
750
views
DiffBind issue: zero values for all peaks in one chromosome
DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
1
vote
6
replies
2.3k
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind dba.count
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
1
vote
1
reply
1.1k
views
Input format for `combinations` in `hashedDrops`
DropletUtils
updated 4.0 years ago by ★ 29k • written 4.0 years ago by ▴ 280
0
votes
0
replies
1.0k
views
confused interpreting results from scanBam in RSamtools
Rsamtools Rsa
4.0 years ago sara • 0
2
votes
2
replies
1.3k
views
universalmotif, question about enrich_motifs function and number of hits returned
universalmotif scanning enrich_motifs PWM
4.0 years ago alexandre.blais ▴ 50
0
votes
4
replies
1.9k
views
DE analysis model matrix for paired samples
NanoStringNCTools DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
0
votes
0
replies
904
views
Color of 2nd exon
GViz
4.0 years ago underscore • 0
2
votes
3
replies
2.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
3
votes
6
replies
3.3k
views
How to use subjunc for differential splicing analysis?
subjunc edgeR
4.0 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.3k
views
catchKallisto results are not counts
DifferentialSplicingWorkflow catchKallisto edgeR DifferentialSplicing
4.0 years ago Assa Yeroslaviz ★ 1.5k
0
votes
11
replies
2.6k
views
Trying to follow a gene set analyisis in R
roast-function
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
1
reply
1.9k
views
SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 4.0 years ago by ▴ 890 • written 4.1 years ago by • 0
0
votes
0
replies
1.1k
views
Rsamtools and data.table OR advice of packages
data.table Rsamtools NGS
4.0 years ago sara • 0
1
vote
1
reply
1.3k
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
1
reply
1.4k
views
Change the interval of bed file
mappability bed python
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
1
vote
1
reply
1.4k
views
Gviz DataTrack data transformation on the fly
aggregation Gviz DataTrack
updated 4.0 years ago by ▴ 750 • written 4.0 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 3.9 years ago by 21k • written 4.0 years ago by ▴ 10
0
votes
0
replies
2.1k
views
下载org.Hs.eg.db,以及无法联网
quiet=T):InternetOpenUrl失败:’无法与服务器建立连接' 报错描述：Warningmessage:Indownload.file(xml.url xml.target
4.0 years ago LeeYusheng • 0
0
votes
0
replies
1.6k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
7
replies
2.0k
views
Uniform window size for different genes
ggbio
4.0 years ago rbenel ▴ 50
0
votes
1
reply
1.3k
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
vote
4
replies
2.4k
views
Issue with selectively labelling genes in the Enhanced Volcano package
EnhancedVolcano
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 10
0
votes
0
replies
1.5k
views
SNPRelate handling of missing genotypes
SNPRelate
4.0 years ago serpalma.v ▴ 60
0
votes
2
replies
1.7k
views
graphite package SSL certificate
graphite
4.1 years ago • updated 4.0 years ago x • 0
0
votes
0
replies
1.4k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
4.0 years ago Sebastian Lewandowski • 0
46,712 results • Page 101 of 935
Recent ...
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Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
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Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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Answer: Where do the filename come from in the LOLA datasets?
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