Showing : RSEM • reset
1
vote
7
replies
197
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
updated 1 day ago by 37k • written 9 days ago by • 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
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
1
vote
4
replies
568
views
TCGA data analysis
RSEM
15 months ago • updated 14 months ago lily ▴ 20
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
0
votes
2
replies
634
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
5
votes
6
replies
967
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
2
replies
607
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
19 months ago harelarik ▴ 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
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
0
votes
8
replies
645
views
Importing RSEM with tximport
tximport RSEM import error
updated 22 months ago by 37k • written 22 months ago by ▴ 50
2
votes
2
replies
409
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 23 months ago by 37k • written 23 months ago by ▴ 20
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
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
341
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
2.5 years ago YH • 0
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
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
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
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
4
replies
644
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
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
0
votes
0
replies
495
views
RSEM output in txtimport
RSEM txtimport
4.1 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 4.1 years ago by 37k • written 4.1 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
2
votes
2
replies
574
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
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
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
2
replies
915
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
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
11
replies
2.4k
views
Tximport with RSEM error
RSEM
updated 4.7 years ago by ▴ 100 • written 4.7 years ago by ▴ 10
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
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
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
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
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
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
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
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
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
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
0
votes
8
replies
1.4k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
5.9 years ago a.guerra • 0
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
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
1
vote
3
replies
1.5k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
6.1 years ago Hugo Varet ▴ 80
44 results • Page 1 of 1
Recent ...
Replies
Comment: Error: BiocParallel errors by lxl13260684135 • 0
I came across the same problem, have you solved it?
Answer: How to get DESeq2 results for a list of genes by ATpoint ★ 1.3k
Standard rules apply for filtering in R. If the genes are the rownames of the results object `res` then: res[my_ges,] or if the colu…
Answer: ComplexHeatmap: Change font size of annotation axis values by nalaspina • 0
Someone on the original post was kind enough to provide the answer (in bold below): row_ha = rowAnnotation(foo2 = runif(10), bar2 = anno…
Answer: setting sizeFactors from scran :: caculateSumFactors. by ATpoint ★ 1.3k
You can conveniently convert your SingleCellExperiment to a DESeqDataSet, see https://bioconductor.org/packages/devel/bioc/vignettes/scran/…
Comment: Combine GRanges(List) to a single GRanges with unified breakpoints by Rodrigo • 0
@malcolm-cook-6293, thank you for your response, I'm working through your code as we speak.
Votes
Answer: setting sizeFactors from scran :: caculateSumFactors.
Answer: ComplexHeatmap: Change font size of annotation axis values
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
A: svaseq: how many and which surrogate variables to pick
A: svaseq: how many and which surrogate variables to pick
Awards • All
Scholar to jaro.slamecka ▴ 130
Scholar to James W. MacDonald 60k
Teacher to Gordon Smyth 45k
Popular Question to Kelen • 0
Popular Question to woongjaej • 0
Locations • All
United States, 1 minute ago
San Diego, 7 minutes ago
United States, 16 minutes ago
China, 1 hour ago
Germany, 1 hour ago
Traffic: 190 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6