Showing : RSEM • reset
0
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165
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Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
6 months ago svlachavas ▴ 780
5
votes
5
replies
9.4k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 10 months ago by 36k • written 5.4 years ago by ▴ 10
1
vote
4
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531
views
TCGA data analysis
RSEM
13 months ago lily ▴ 20
0
votes
1
reply
308
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 16 months ago by 36k • written 16 months ago by • 0
0
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2
replies
580
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
17 months ago harelarik ▴ 50
5
votes
6
replies
897
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Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
17 months ago svlachavas ▴ 780
0
votes
2
replies
564
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
18 months ago harelarik ▴ 50
1
vote
4
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453
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tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 18 months ago by 36k • written 20 months ago by • 0
6
votes
13
replies
1.6k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 21 months ago by 45k • written 21 months ago by ▴ 50
0
votes
8
replies
595
views
Importing RSEM with tximport
tximport RSEM import error
updated 21 months ago by 36k • written 21 months ago by ▴ 50
2
votes
2
replies
380
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 21 months ago by 36k • written 21 months ago by ▴ 20
1
vote
3
replies
308
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RSEM and Tximport
RSEM tximport deseq2
updated 23 months ago by 59k • written 23 months ago by • 0
4
votes
7
replies
1.4k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 2.0 years ago by 3.5k • written 2.0 years ago by • 0
0
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0
replies
325
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
2.4 years ago YH • 0
0
votes
6
replies
1.4k
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
3.7 years ago loliveira • 0
0
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0
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527
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
3.8 years ago kicheol.kim • 0
1
vote
0
replies
1.4k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
3.9 years ago • updated 3.8 years ago kicheol.kim • 0
0
votes
1
reply
405
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 3.9 years ago by 36k • written 3.9 years ago by • 0
1
vote
4
replies
625
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 3.9 years ago by 36k • written 3.9 years ago by ▴ 50
0
votes
5
replies
678
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 3.9 years ago by 36k • written 3.9 years ago by • 0
0
votes
0
replies
481
views
RSEM output in txtimport
RSEM txtimport
4.0 years ago gat2010 • 0
0
votes
8
replies
1.5k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 4.0 years ago by 36k • written 4.0 years ago by • 0
1
vote
18
replies
2.3k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
4.1 years ago stephan.emmrich • 0
2
votes
2
replies
557
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
3
votes
13
replies
1.2k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
4.3 years ago tim.ivanov.92 • 0
0
votes
1
reply
711
views
Data object format for deseq2
deseq2 R RSEM
updated 4.3 years ago by 36k • written 4.3 years ago by • 0
1
vote
2
replies
895
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 10
3
votes
4
replies
2.2k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 4.5 years ago by 36k • written 4.5 years ago by ▴ 10
1
vote
11
replies
2.4k
views
Tximport with RSEM error
RSEM
updated 4.6 years ago by ▴ 100 • written 4.6 years ago by ▴ 10
2
votes
7
replies
1.0k
views
Obtaining transcript names in RSEM
tximport rsem
updated 4.7 years ago by 36k • written 4.7 years ago by ▴ 20
0
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2
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745
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 4.7 years ago by 36k • written 4.7 years ago by ▴ 10
3
votes
1
reply
1.0k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 90
0
votes
1
reply
1.2k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 4.8 years ago by 45k • written 4.8 years ago by • 0
1
vote
3
replies
1.4k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 4.9 years ago by 59k • written 4.9 years ago by ▴ 90
6
votes
5
replies
2.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 5.1 years ago by 45k • written 5.1 years ago by ▴ 20
0
votes
0
replies
1.9k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
5.2 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
1.3k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 5.3 years ago by 36k • written 5.3 years ago by • 0
25
votes
37
replies
7.5k
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 5.4 years ago by 45k • written 5.4 years ago by ▴ 780
5
votes
9
replies
4.6k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
5.7 years ago komal.rathi ▴ 100
0
votes
8
replies
1.3k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
5.8 years ago a.guerra • 0
6
votes
4
replies
3.0k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 5.9 years ago by 45k • written 5.9 years ago by ▴ 90
4
votes
7
replies
1.0k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 5.9 years ago by 59k • written 5.9 years ago by ★ 1.5k
1
vote
3
replies
1.5k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
6.0 years ago Hugo Varet ▴ 80
43 results • Page 1 of 1
Recent ...
Replies
Answer: help understanding limma by Gordon Smyth 45k
It is obvious that you haven't exported and read the correct intensity data, as you admit yourself in your question. I don't know what the …
Answer: performing the differential binding in ChIP-seq by etiennedanis • 0
DiffBind https://bioconductor.org/packages/release/bioc/html/DiffBind.html
Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
Did you see the part of the vignette where we talk about this? https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Hi Michael, thanks for your reply. One more question. If the qvalue (and pvalue) for all DTEs are the same, the Volcano plot will look lik…
Comment: R: problem with running time-series analysis software: Mfuzz by soda ▴ 80
I have solved this problem by myself. My data.frame is not suitable for Mfuzz.
Votes
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
C: DESeq2 - Differences between plotCounts and normalized counts
C: DESEq2 - Change reference level change "Contrasts" results
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