Showing : RSEM • reset
0
votes
4
replies
529
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 months ago NB • 0
2
votes
13
replies
5.5k
views
Tximport with RSEM error
RSEM
updated 4 months ago by 43k • written 7.4 years ago by ▴ 20
1
vote
4
replies
1.4k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 22 months ago by • 0
0
votes
1
reply
830
views
tximport error with rsem files
rsem tximport
updated 15 months ago by ★ 4.7k • written 15 months ago by • 0
1
vote
4
replies
2.2k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 24 months ago by 52k • written 24 months ago by ▴ 10
1
vote
2
replies
997
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.0 years ago Yang Shi ▴ 10
2
votes
3
replies
1.8k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.3 years ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
2.0k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
2.4 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 2.6 years ago by 43k • written 2.6 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
2.3k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
2.7 years ago Yang Shi ▴ 10
2
votes
4
replies
2.3k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.7 years ago Yang Shi ▴ 10
6
votes
13
replies
7.0k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.7 years ago by 52k • written 4.6 years ago by ▴ 60
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 Kelen ▴ 10
0
votes
0
replies
911
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
10
votes
5
replies
19k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 3.7 years ago by 43k • written 8.2 years ago by ▴ 30
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 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
2
replies
1.8k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.3 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
4.3 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 4.4 years ago by 43k • written 4.5 years ago by • 0
0
votes
8
replies
2.4k
views
Importing RSEM with tximport
tximport RSEM import error
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 60
2
votes
2
replies
1.3k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 20
1
vote
3
replies
1.1k
views
RSEM and Tximport
RSEM tximport deseq2
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
4
votes
7
replies
5.1k
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
1.1k
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
6.5 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
6.7 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
6.7 years ago kicheol.kim • 0
0
votes
1
reply
1.0k
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
vote
4
replies
1.6k
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
1.7k
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
1.1k
views
RSEM output in txtimport
RSEM txtimport
6.8 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
4.0k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.0 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 7.1 years ago by • 0
3
votes
13
replies
2.9k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
7.1 years ago tim.ivanov.92 • 0
0
votes
1
reply
1.5k
views
Data object format for deseq2
deseq2 R RSEM
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
vote
2
replies
2.3k
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
4.4k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
2
votes
7
replies
2.6k
views
Obtaining transcript names in RSEM
tximport rsem
updated 7.5 years ago by 43k • written 7.5 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
1.8k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 7.6 years ago by 52k • written 7.6 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
3.1k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 7.7 years ago by 68k • written 7.7 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
2.9k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
8.0 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
2.2k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 8.1 years ago by 43k • written 8.1 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 8.2 years ago by 52k • written 8.2 years ago by ▴ 840
50 results • Page 1 of 1
Recent ...
Replies
Answer: affy::rma results doesn't match with ncbi website by ATpoint ★ 4.7k
Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…
Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
Awards • All
Popular Question to igor ▴ 50
Popular Question to xiaofeiwang198266 • 0
Scholar to shepherl 4.1k
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 52k
Locations • All
Germany, 23 minutes ago
Iran, 38 minutes ago
United States, 3 hours ago
UPF, Barcelona, Spain, 4 hours ago
Japan, 5 hours ago
Traffic: 702 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