Showing : RSEM • reset
25
votes
37
replies
7.6k
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 5.5 years ago by 45k • written 5.5 years ago by ▴ 800
0
votes
8
replies
1.4k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
5.9 years ago a.guerra • 0
5
votes
9
replies
4.7k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
5.8 years ago komal.rathi ▴ 100
6
votes
4
replies
3.1k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 6.0 years ago by 45k • written 6.0 years ago by ▴ 90
6
votes
13
replies
1.7k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 22 months ago by 45k • written 22 months ago by ▴ 50
1
vote
3
replies
331
views
RSEM and Tximport
RSEM tximport deseq2
updated 2.0 years ago by 60k • written 2.0 years ago by • 0
3
votes
13
replies
1.2k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
4.4 years ago tim.ivanov.92 • 0
1
vote
3
replies
1.5k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
6.2 years ago • updated 6.1 years ago Hugo Varet ▴ 80
2
votes
2
replies
575
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 4.3 years ago by • 0 • written 4.3 years ago by • 0
2
votes
7
replies
1.1k
views
Obtaining transcript names in RSEM
tximport rsem
updated 4.8 years ago by 37k • written 4.8 years ago by ▴ 20
1
vote
11
replies
2.4k
views
Tximport with RSEM error
RSEM
updated 4.7 years ago by ▴ 100 • written 4.7 years ago by ▴ 10
3
votes
4
replies
2.3k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 10
1
vote
2
replies
916
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 4.5 years ago by ★ 27k • written 4.5 years ago by ▴ 10
0
votes
1
reply
724
views
Data object format for deseq2
deseq2 R RSEM
updated 4.5 years ago by 37k • written 4.5 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
4.3 years ago stephan.emmrich • 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 4.1 years ago by 37k • written 4.1 years ago by • 0
0
votes
5
replies
703
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 4.0 years ago by 37k • written 4.0 years ago by • 0
1
vote
4
replies
645
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 4.0 years ago by 37k • written 4.0 years ago by ▴ 50
0
votes
1
reply
413
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 4.0 years ago by 37k • written 4.0 years ago by • 0
1
vote
7
replies
205
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
updated 3 days ago by 37k • written 10 days ago by • 0
4
votes
7
replies
1.1k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 6.0 years ago by 60k • written 6.0 years ago by ★ 1.5k
7
votes
5
replies
9.7k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 12 months ago by 37k • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.3k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 5.4 years ago by 37k • written 5.4 years ago by • 0
6
votes
5
replies
2.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 5.2 years ago by 45k • written 5.2 years ago by ▴ 20
1
vote
3
replies
1.5k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 5.0 years ago by 60k • written 5.0 years ago by ▴ 90
0
votes
1
reply
1.3k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 4.9 years ago by 45k • written 4.9 years ago by • 0
3
votes
1
reply
1.0k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 4.9 years ago by 45k • written 4.9 years ago by ▴ 90
0
votes
2
replies
756
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 4.8 years ago by 37k • written 4.8 years ago by ▴ 10
2
votes
2
replies
411
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 23 months ago by 37k • written 23 months ago by ▴ 20
0
votes
8
replies
646
views
Importing RSEM with tximport
tximport RSEM import error
updated 22 months ago by 37k • written 22 months ago by ▴ 50
1
vote
4
replies
474
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 20 months ago by 37k • written 21 months ago by • 0
0
votes
2
replies
608
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
19 months ago harelarik ▴ 50
5
votes
6
replies
971
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
19 months ago svlachavas ▴ 800
0
votes
1
reply
343
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 18 months ago by 37k • written 18 months ago by • 0
1
vote
4
replies
569
views
TCGA data analysis
RSEM
15 months ago lily ▴ 20
0
votes
6
replies
1.5k
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
3.8 years ago loliveira • 0
4
votes
7
replies
1.5k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 2.1 years ago by 3.6k • written 2.1 years ago by • 0
0
votes
0
replies
540
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
4.0 years ago kicheol.kim • 0
0
votes
0
replies
2.0k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
5.3 years ago panagiotis.mokos ▴ 40
0
votes
0
replies
342
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
2.5 years ago YH • 0
0
votes
2
replies
635
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
19 months ago harelarik ▴ 50
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
4.0 years ago kicheol.kim • 0
0
votes
0
replies
195
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
7 months ago svlachavas ▴ 800
0
votes
0
replies
495
views
RSEM output in txtimport
RSEM txtimport
4.1 years ago gat2010 • 0
44 results • Page 1 of 1
Recent ...
Replies
Comment: For loop for DESeq2 by krushnach80 • 0
what is the solution?
Comment: How to get DESeq2 results for a list of genes by ATpoint ★ 1.3k
That's a problem related to your lack of R basics, neither DESeq2 or Bioconductor software/technical problem. Please learn R basics first. …
Comment: How to get DESeq2 results for a list of genes by Lucía ▴ 10
Hi, thank you! Unfortunately that doesn't work. The first option gives me this error: ``` # Extracting for list my_genes <- read.delim("di…
Answer: Error by ATpoint ★ 1.3k
https://github.com/conda-forge/rpy2-feedstock/issues/1
Comment: Error: BiocParallel errors by lxl13260684135 • 0
I came across the same problem, have you solved it?
Votes
A: How to handle the change in resultsNames() for DESeq2 ?
A: How to handle the change in resultsNames() for DESeq2 ?
C: How to handle the change in resultsNames() for DESeq2 ?
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
Answer: Although I successfully installed the package "simpleaffy'' , I cannot library i
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