Showing : rsem • reset
25
votes
37
replies
11k
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 7.3 years ago by 50k • written 7.3 years ago by ▴ 830
2
votes
18
replies
3.5k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.1 years ago stephan.emmrich ▴ 10
6
votes
13
replies
5.2k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 21 months ago by 50k • written 3.7 years ago by ▴ 60
3
votes
13
replies
2.4k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
6.2 years ago tim.ivanov.92 • 0
2
votes
11
replies
4.4k
views
Tximport with RSEM error
RSEM
updated 6.5 years ago by ▴ 120 • written 6.5 years ago by ▴ 20
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
7.7 years ago komal.rathi ▴ 120
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago Yang Shi ▴ 10
0
votes
8
replies
2.6k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
0
votes
8
replies
2.0k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
7.7 years ago a.guerra • 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
0
votes
8
replies
1.8k
views
Importing RSEM with tximport
tximport RSEM import error
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 60
2
votes
7
replies
2.0k
views
Obtaining transcript names in RSEM
tximport rsem
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 20
4
votes
7
replies
1.7k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 7.9 years ago by 65k • written 7.9 years ago by ★ 1.5k
4
votes
7
replies
4.0k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
0
votes
6
replies
2.5k
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
5.6 years ago loliveira • 0
6
votes
6
replies
2.3k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
3.4 years ago svlachavas ▴ 830
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
21 months ago Yang Shi ▴ 10
0
votes
5
replies
1.3k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
9
votes
5
replies
16k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 2.9 years ago by 41k • written 7.4 years ago by ▴ 30
4
votes
5
replies
2.2k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 20 months ago by 41k • written 21 months ago by ▴ 10
6
votes
5
replies
3.9k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.1 years ago by 50k • written 7.1 years ago by ▴ 20
1
vote
4
replies
1.0k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 3.5 years ago by 41k • written 3.6 years ago by • 0
1
vote
4
replies
1.2k
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 5.9 years ago by 41k • written 5.9 years ago by ▴ 50
1
vote
4
replies
1.3k
views
TCGA data analysis
RSEM
3.1 years ago lily ▴ 20
3
votes
4
replies
3.7k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 10
2
votes
4
replies
1.4k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
21 months ago Yang Shi ▴ 10
6
votes
4
replies
4.2k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 90
1
vote
4
replies
1.3k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 13 months ago by 50k • written 13 months ago by ▴ 10
1
vote
3
replies
2.1k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
8.0 years ago Hugo Varet ▴ 80
1
vote
3
replies
2.6k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 6.8 years ago by 65k • written 6.8 years ago by ▴ 110
1
vote
3
replies
849
views
RSEM and Tximport
RSEM tximport deseq2
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
1
vote
3
replies
897
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 10 months ago by • 0 • written 12 months ago by • 0
0
votes
3
replies
1.3k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
18 months ago Niveditha ▴ 20
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
638
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
13 months ago Yang Shi ▴ 10
1
vote
2
replies
1.7k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
3.5 years ago harelarik ▴ 60
2
votes
2
replies
1.1k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 6.2 years ago by • 0 • written 6.2 years ago by • 0
0
votes
2
replies
1.4k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
3.4 years ago harelarik ▴ 60
2
votes
2
replies
961
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 20
0
votes
1
reply
818
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
0
votes
1
reply
942
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
0
votes
1
reply
1.3k
views
Data object format for deseq2
deseq2 R RSEM
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
0
votes
1
reply
353
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
3
votes
1
reply
1.5k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 110
0
votes
1
reply
1.8k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
0
votes
1
reply
1.8k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 6.8 years ago by 50k • written 6.8 years ago by • 0
0
votes
0
replies
2.6k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
7.1 years ago panagiotis.mokos ▴ 40
1
vote
0
replies
2.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
50 results • Page 1 of 1
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Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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