Showing : r • reset
0
votes
17
replies
970
views
How to check linear model
modalmatrix limma R linear
7 months ago • updated 6 months ago Jitendra ▴ 10
3
votes
16
replies
1.5k
views
Atena package - error (new user)
RNAseq R Atena
11 months ago • updated 7 months ago lalanis1 • 0
2
votes
14
replies
6.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 7 months ago by • 0 • written 6.1 years ago by ▴ 110
0
votes
13
replies
1.6k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
6 months ago Laia ▴ 10
8
votes
11
replies
9.6k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 4 months ago by • 0 • written 6.3 years ago by ▴ 10
2
votes
9
replies
789
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 7 months ago by 63k • written 7 months ago by • 0
7
votes
9
replies
2.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 8 months ago by ★ 2.8k • written 4.4 years ago by ▴ 10
5
votes
8
replies
1.3k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
12 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
4
votes
8
replies
1.3k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 3 months ago by 48k • written 9 months ago by ▴ 20
1
vote
7
replies
825
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 9 months ago by 3.5k • written 9 months ago by • 0
2
votes
7
replies
8.2k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 9 days ago by 48k • written 14 months ago by ▴ 20
3
votes
7
replies
952
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 10 months ago by 48k • written 10 months ago by • 0
4
votes
6
replies
716
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
9 months ago Abdul ▴ 20
0
votes
6
replies
978
views
No differentially expressed genes after DESeq
DESeq2 R
12 months ago • updated 11 months ago Zach • 0
3
votes
6
replies
3.5k
views
WGCNA gene significance and module membership
WGCNA R
updated 10 months ago by ★ 2.8k • written 3.9 years ago by • 0
2
votes
6
replies
831
views
DMRcate
DMRcate R DMRcatedata Markdown
7 months ago yr542 • 0
2
votes
5
replies
467
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
1.3k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 11 months ago by ★ 3.7k • written 11 months ago by ▴ 20
4
votes
5
replies
3.4k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 8 months ago by • 0 • written 14 months ago by ▴ 50
2
votes
5
replies
2.3k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 11 months ago by 40k • written 2.2 years ago by • 0
0
votes
4
replies
432
views
Unable to install BiocManager
Biocmanager R
updated 5 months ago by ▴ 50 • written 5 months ago by • 0
2
votes
4
replies
1.2k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 9 months ago by • 0
4
votes
4
replies
1.3k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 4 months ago by • 0 • written 11 months ago by ▴ 20
7
votes
4
replies
4.7k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 10 months ago by ▴ 10 • written 16 months ago by ▴ 40
0
votes
4
replies
421
views
how to extract list in quantile in R
R quantile list
6 months ago sat • 0
1
vote
4
replies
1.1k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 5 months ago by 48k • written 4.8 years ago by • 0
2
votes
4
replies
1.2k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 5 months ago by • 0 • written 4.8 years ago by • 0
2
votes
4
replies
2.0k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
9 months ago mohammedtoufiq91 ▴ 10
0
votes
4
replies
517
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
7 months ago Dr. • 0
2
votes
4
replies
1.7k
views
running msa (msa) aborts R session
msa alignment r software error
written 5.8 years ago by • 0
0
votes
4
replies
382
views
Combine RNA-seq
BatchEffect R rnaseq
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
0
votes
4
replies
681
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
10 months ago Amit Indap ▴ 10
7
votes
3
replies
3.6k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 10 months ago by 48k • written 4.6 years ago by ▴ 70
0
votes
3
replies
1.3k
views
How to extract / pull out each row(a.k.a, single genome interval ) from given bed files by row by row for meta analysis?
r bioinformatics peakset
updated 5 months ago by • 0 • written 7.7 years ago by ▴ 80
3
votes
3
replies
3.6k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 3 months ago by ★ 3.7k • written 3.4 years ago by • 0
1
vote
3
replies
2.0k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 7 months ago by 3.8k • written 3.2 years ago by • 0
0
votes
3
replies
670
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
11 months ago Madiha • 0
2
votes
3
replies
653
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 10 months ago by 48k • written 10 months ago by • 0
0
votes
3
replies
518
views
batch effect in EPIC array data
statistics Epigenetics R
updated 7 months ago by ▴ 720 • written 7 months ago by ▴ 10
0
votes
3
replies
1.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 6 months ago by ★ 3.7k • written 7 months ago by • 0
0
votes
3
replies
668
views
How to write a script for identifying associate gene id
bash r bingo
2.2 years ago • updated 9 months ago abhisek001 • 0
0
votes
3
replies
495
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 8 months ago by 63k • written 8 months ago by • 0
0
votes
3
replies
646
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 9 months ago by ▴ 150 • written 9 months ago by • 0
1
vote
3
replies
397
views
tximport error
tximport r
updated 5 months ago by 40k • written 5 months ago by • 0
0
votes
2
replies
664
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 8 months ago by • 0 • written 10 months ago by • 0
0
votes
2
replies
699
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 7 months ago by 48k • written 8 months ago by • 0
0
votes
2
replies
625
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 9 months ago by ★ 3.4k • written 10 months ago by • 0
0
votes
2
replies
811
views
Properly constructing a hypergeometric test
overrepresentation overlap R hypergeometric
updated 11 months ago by ★ 3.4k • written 11 months ago by ▴ 160
1
vote
2
replies
511
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
10 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
194
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
8 weeks ago Miguel • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Answer: What MetaPhlAn3 database was used in cMD 3?
Comment: Speeding up of DelayedArray::write_block()
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