Showing : RSEM • reset
0
votes
4
replies
455
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
9 weeks ago NB • 0
0
votes
1
reply
751
views
tximport error with rsem files
rsem tximport
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
vote
4
replies
1.3k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 21 months ago by • 0
1
vote
4
replies
2.1k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 22 months ago by 52k • written 22 months ago by ▴ 10
1
vote
2
replies
937
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
22 months ago Yang Shi ▴ 10
2
votes
3
replies
1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.2 years ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
1.8k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
2.3 years ago Niveditha ▴ 20
4
votes
5
replies
2.9k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
5
votes
9
replies
2.4k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.5 years ago Yang Shi ▴ 10
5
votes
6
replies
2.2k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
2.5 years ago Yang Shi ▴ 10
2
votes
4
replies
2.1k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.5 years ago Yang Shi ▴ 10
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.6 years ago Kelen ▴ 10
0
votes
0
replies
877
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
3.2 years ago svlachavas ▴ 840
1
vote
4
replies
1.6k
views
TCGA data analysis
RSEM
3.8 years ago lily ▴ 20
0
votes
1
reply
1.1k
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
votes
2
replies
1.7k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.2 years ago harelarik ▴ 60
6
votes
6
replies
2.7k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.2 years ago svlachavas ▴ 840
0
votes
2
replies
1.9k
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
4.2 years ago harelarik ▴ 60
1
vote
4
replies
1.4k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.2 years ago by 43k • written 4.4 years ago by • 0
6
votes
13
replies
6.6k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.5 years ago by 52k • written 4.4 years ago by ▴ 60
0
votes
8
replies
2.3k
views
Importing RSEM with tximport
tximport RSEM import error
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 60
2
votes
2
replies
1.2k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 20
1
vote
3
replies
1.0k
views
RSEM and Tximport
RSEM tximport deseq2
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
4
votes
7
replies
4.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
votes
0
replies
1.0k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.1 years ago YH • 0
0
votes
6
replies
2.8k
views
Large fold changes after deseq2 when one condition has two zeros and small number the other condition has two zeros and a large number
rnaseq rsem deseq2
6.3 years ago loliveira • 0
0
votes
0
replies
1.1k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.5 years ago kicheol.kim • 0
1
vote
0
replies
2.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.6 years ago • updated 6.5 years ago kicheol.kim • 0
0
votes
1
reply
982
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
4
replies
1.5k
views
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 50
0
votes
5
replies
1.6k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
0
replies
1.0k
views
RSEM output in txtimport
RSEM txtimport
6.7 years ago gat2010 • 0
0
votes
8
replies
2.9k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
votes
18
replies
3.9k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.8 years ago stephan.emmrich ▴ 10
2
votes
2
replies
1.3k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 6.9 years ago by • 0 • written 6.9 years ago by • 0
3
votes
13
replies
2.8k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
7.0 years ago tim.ivanov.92 • 0
0
votes
1
reply
1.5k
views
Data object format for deseq2
deseq2 R RSEM
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
vote
2
replies
2.1k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
3
votes
4
replies
4.3k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
2
votes
13
replies
5.3k
views
Tximport with RSEM error
RSEM
updated 11 weeks ago by 43k • written 7.3 years ago by ▴ 20
2
votes
7
replies
2.4k
views
Obtaining transcript names in RSEM
tximport rsem
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
1
vote
2
replies
1.7k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
3
votes
1
reply
1.7k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 120
0
votes
1
reply
2.0k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 7.5 years ago by 52k • written 7.5 years ago by • 0
1
vote
3
replies
3.0k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 7.6 years ago by 67k • written 7.6 years ago by ▴ 120
6
votes
5
replies
4.4k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.8 years ago by 52k • written 7.8 years ago by ▴ 20
0
votes
0
replies
2.8k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
7.9 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
2.1k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
25
votes
37
replies
12k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 8.1 years ago by 52k • written 8.1 years ago by ▴ 840
10
votes
5
replies
18k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 3.6 years ago by 43k • written 8.1 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
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FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
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Thanks James!
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Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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