Showing : rsem • reset
0
votes
4
replies
483
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 months ago NB • 0
0
votes
1
reply
795
views
tximport error with rsem files
rsem tximport
updated 14 months ago by ★ 4.7k • written 14 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 23 months ago by 52k • written 23 months ago by ▴ 10
1
vote
2
replies
971
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
23 months ago Yang Shi ▴ 10
2
votes
3
replies
1.8k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.2 years ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
1.9k
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
3.0k
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
2.5k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.6 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
2.6 years ago Yang Shi ▴ 10
2
votes
4
replies
2.2k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.6 years ago Yang Shi ▴ 10
2
votes
8
replies
2.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.7 years ago • updated 2.6 years ago Kelen ▴ 10
0
votes
0
replies
894
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
3.3 years ago svlachavas ▴ 840
1
vote
4
replies
1.7k
views
TCGA data analysis
RSEM
3.9 years ago lily ▴ 20
0
votes
1
reply
1.2k
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
4.3 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 4.3 years ago by 43k • written 4.4 years ago by • 0
6
votes
13
replies
6.8k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.6 years ago by 52k • written 4.5 years ago by ▴ 60
0
votes
8
replies
2.4k
views
Importing RSEM with tximport
tximport RSEM import error
updated 4.5 years ago by 43k • written 4.5 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
1.1k
views
RSEM and Tximport
RSEM tximport deseq2
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
4
votes
7
replies
5.0k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
0
votes
0
replies
1.0k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.2 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
6.4 years ago loliveira • 0
0
votes
0
replies
1.2k
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 kicheol.kim • 0
1
vote
0
replies
2.3k
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 kicheol.kim • 0
0
votes
1
reply
1.0k
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 6.7 years ago by 43k • written 6.7 years ago by ▴ 50
0
votes
5
replies
1.6k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 6.7 years ago by 43k • written 6.7 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
3.0k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 6.8 years ago by 43k • written 6.8 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
6.9 years ago stephan.emmrich ▴ 10
2
votes
2
replies
1.4k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 7.0 years ago by • 0 • written 7.0 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 7.1 years ago by 43k • written 7.1 years ago by • 0
1
vote
2
replies
2.2k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.2 years ago by ★ 28k • written 7.2 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
5.4k
views
Tximport with RSEM error
RSEM
updated 3 months ago by 43k • written 7.3 years ago by ▴ 20
2
votes
7
replies
2.5k
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
1.8k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 7.5 years ago by 43k • written 7.5 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
2.1k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 7.6 years ago by 52k • written 7.6 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 68k • written 7.6 years ago by ▴ 120
6
votes
5
replies
4.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.9 years ago by 52k • written 7.9 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
13k
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
19k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 3.6 years ago by 43k • written 8.2 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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