Showing : counts • reset
3
votes
1
reply
2.2k
views
log2 of normalized counts for further analyzes
DESeq2 log2 normalized counts
updated 21 months ago by 67k • written 21 months ago by ▴ 10
2
votes
5
replies
1.9k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 months ago by 42k • written 23 months ago by • 0
2
votes
1
reply
1.8k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by ▴ 10
1
vote
5
replies
11k
views
is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by ▴ 10
0
votes
3
replies
1.3k
views
dealing with outliers (deseq2)
maxcooks outliers zero counts DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
small RNA counts
counts SmallRNA Normalization
updated 2.9 years ago by ▴ 80 • written 3.0 years ago by ▴ 30
4
votes
4
replies
5.7k
views
FeatureCounts
counts subread RNASeq featurecounts
3.0 years ago k___ ▴ 30
0
votes
2
replies
3.6k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
1
vote
8
replies
2.3k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq DESeq2 outlier counts DE analysis
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
2
votes
4
replies
5.3k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
5.6 years ago • updated 4.7 years ago Mozart ▴ 30
0
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0
replies
855
views
using gene expression matrix for TCseq package to cluster genes
TCseq microwarray cluster counts normalization
5.3 years ago bioyas ▴ 10
5
votes
3
replies
1.5k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.7 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
2
votes
5
replies
13k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 13 months ago by • 0 • written 5.9 years ago by • 0
0
votes
7
replies
1.6k
views
Results table completely wrong for specified contrast of
DESeq2 logfoldchange counts
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 40
0
votes
7
replies
2.7k
views
Count filter for differential expression
edger limma counts
updated 6.0 years ago by 51k • written 6.0 years ago by • 0
2
votes
4
replies
2.3k
views
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
deseq2 edger fpkm counts fc
updated 6.2 years ago by 51k • written 6.2 years ago by • 0
1
vote
2
replies
1.4k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 6.2 years ago by 51k • written 6.2 years ago by • 0
0
votes
3
replies
3.8k
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 6.4 years ago by ★ 1.1k • written 6.4 years ago by • 0
2
votes
3
replies
2.9k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 3.5 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
1
vote
1
reply
1.1k
views
How to compare RNA-seq counts matrices from different aligners ?
rnaseq counts alignement
6.7 years ago Aurora ▴ 20
2
votes
3
replies
4.2k
views
Deseq2: padj value changes with varying alpha
deseq2 counts rnaseq
updated 7.1 years ago by 42k • written 7.1 years ago by ▴ 10
0
votes
5
replies
7.1k
views
unable to find an inherited method for function counts for signature DESeqTransform
deseq2 counts DESeqtransform variance deviation
updated 7.1 years ago by 42k • written 7.1 years ago by • 0
0
votes
3
replies
1.7k
views
DESeq2 ComputeSumFactors extract normalized counts
deseq2 normalization counts
updated 7.2 years ago by 42k • written 7.2 years ago by • 0
0
votes
0
replies
1.0k
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
7.2 years ago lirongrossmann ▴ 80
4
votes
2
replies
2.0k
views
Help: extract counts from RNA-seq .bam/.bai files
counts edger
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 80
6
votes
4
replies
3.4k
views
Can edgeR TMM normalization be used for other count data?
edgeR tmm normalization counts
updated 7.6 years ago by 67k • written 7.6 years ago by ▴ 40
0
votes
1
reply
1.6k
views
IRanges object from count matrix
genomicranges iranges featurecounts counts rnaseq
updated 7.8 years ago by 16k • written 7.8 years ago by ★ 1.5k
0
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2
replies
1.3k
views
small RNAs quantification
smallrna counts
8.2 years ago ribioinfo ▴ 100
2
votes
1
reply
4.3k
views
DESeq2 Input format
deseq2 counts
updated 8.2 years ago by 42k • written 8.2 years ago by • 0
1
vote
3
replies
1.5k
views
DESeq2: Do basemean values take into account interaction effects?
deseq2 counts normalized counts
updated 8.3 years ago by ★ 13k • written 8.3 years ago by ▴ 40
1
vote
4
replies
1.5k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
8.4 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
2.2k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2 chipseq counts log2fc error
updated 8.5 years ago by 42k • written 8.5 years ago by • 0
3
votes
1
reply
1.5k
views
window counts in csaw
csaw counts
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
6
votes
12
replies
18k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.6 years ago by 42k • written 8.6 years ago by ▴ 10
4
votes
3
replies
10k
views
How do I extract read counts from DESeq2
deseq2 counts covariates
updated 8.7 years ago by 42k • written 8.7 years ago by ▴ 10
1
vote
3
replies
3.7k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff
8.8 years ago Jon Bråte ▴ 260
2
votes
4
replies
2.7k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.9 years ago bioprog • 0
2
votes
5
replies
3.1k
views
Limma/DESeq2: Statistic and readcount of biological replicates
normalization limma deseq2 counts
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 90
1
vote
5
replies
2.0k
views
deseq2 normalized data
regression deseq2 counts
updated 9.2 years ago by 42k • written 9.2 years ago by • 0
1
vote
1
reply
5.9k
views
Not full rank design using Deseq2
deseq2 design counts
updated 9.8 years ago by 42k • written 9.8 years ago by ▴ 30
0
votes
1
reply
1.6k
views
DEXSeq error: Count files do not correspond to the flattened annotation file
DEXSeq counts gff
10.0 years ago Assa Yeroslaviz ★ 1.5k
4
votes
5
replies
9.4k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 10
43 results • Page 1 of 1
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Answer: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
Comment: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://www.hayalsohbet.net https://www.yerlichat.com https://www.yerlichat.net https://www.mavisim.net https://www.hayalchat.com http…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Answer: Differene between the Wald and LRT test for time-series gene expression data by James W. MacDonald 67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
Votes
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Allele frequencies for ALL alleles of one SNP ?
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Using Affymetrix Custom Array
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