Showing : rsem • reset
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tximport error importing expected counts file from RSEM
RSEM tximport
10 days ago Muyu • 0 • updated 10 days ago Michael Love 31k
0
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2
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71
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How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
6 weeks ago harelarik • 50
5
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6
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226
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Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
7 weeks ago • updated 6 weeks ago svlachavas • 770
0
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2
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73
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Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
8 weeks ago harelarik • 50
1
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4
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154
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tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
4 months ago m.metsger • 0 • updated 10 weeks ago Michael Love 31k
6
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13
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344
Views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
4 months ago harelarik • 50 • updated 4 months ago Gordon Smyth 41k
0
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8
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141
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Importing RSEM with tximport
tximport RSEM import error
4 months ago harelarik • 50 • updated 4 months ago Michael Love 31k
2
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2
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96
Views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
5 months ago le2336 • 20 • updated 5 months ago Michael Love 31k
1
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3
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71
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RSEM and Tximport
RSEM tximport deseq2
7 months ago pthom010 • 0 • updated 7 months ago James W. MacDonald 55k
4
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7
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243
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Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
8 months ago J. Smith • 0 • updated 8 months ago Kevin Blighe 2.3k
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0
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140
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Is the ballgownrsem function still supported?
ballgown rsem iranges
13 months ago • updated 12 months ago YH • 0
0
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6
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701
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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
2.3 years ago loliveira • 0
0
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0
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327
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IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
2.5 years ago kicheol.kim • 0
1
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0
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969
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IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
2.5 years ago kicheol.kim • 0
0
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1
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263
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Using tximport on RSEM abundance date
rnaseq rsem tximport
2.5 years ago raeganlynn123 • 0 • updated 2.5 years ago Michael Love 31k
1
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4
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407
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
2.6 years ago al-ash • 20 • updated 2.6 years ago Michael Love 31k
0
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5
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413
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countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
2.6 years ago celi0001 • 0 • updated 2.6 years ago Michael Love 31k
0
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0
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317
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RSEM output in txtimport
RSEM txtimport
2.6 years ago gat2010 • 0
0
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8
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892
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Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
2.7 years ago LD • 0 • updated 2.7 years ago Michael Love 31k
1
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18
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1.5k
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Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
2.8 years ago stephan.emmrich • 0
2
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2
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332
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tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
2.9 years ago fresard.laure • 0 • updated 2.9 years ago rosabellascottgm • 0
3
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13
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805
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tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
2.9 years ago tim.ivanov.92 • 0
0
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1
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479
Views
Data object format for deseq2
deseq2 R RSEM
3.0 years ago tim.ivanov.92 • 0 • updated 3.0 years ago Michael Love 31k
1
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2
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618
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RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
3.1 years ago goldberg.jm • 10 • updated 3.1 years ago Aaron Lun ♦ 26k
3
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4
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1.5k
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Importing RSEM transcript-level data using tximport
tximport rsem
3.1 years ago Patrick Kimes • 10 • updated 3.1 years ago Michael Love 31k
1
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11
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1.4k
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Tximport with RSEM error
RSEM
3.2 years ago hs.lansdell • 10 • updated 3.2 years ago k.vitting.seerup • 100
2
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7
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711
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Obtaining transcript names in RSEM
tximport rsem
3.3 years ago deena • 10 • updated 3.3 years ago Michael Love 31k
0
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2
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541
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Using RSEM reads for DESeq2
deseq2 rsem
3.4 years ago deeptiptl74 • 0 • updated 3.4 years ago Michael Love 31k
3
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1
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806
Views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
3.4 years ago Biologist • 90 • updated 3.4 years ago Gordon Smyth 41k
0
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1
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1.0k
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confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
3.5 years ago arubio • 0 • updated 3.5 years ago Gordon Smyth 41k
1
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3
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885
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Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
3.5 years ago Biologist • 90 • updated 3.5 years ago James W. MacDonald 55k
6
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5
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1.8k
Views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
3.8 years ago hrishi27n • 20 • updated 3.8 years ago Gordon Smyth 41k
0
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0
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1.6k
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How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
3.8 years ago panagiotis.mokos • 40
0
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1
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1.0k
Views
RSEM output in DeSeq2
RSEM deseq2 count matrix
3.9 years ago kmeusemann • 0 • updated 3.9 years ago Michael Love 31k
25
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37
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5.7k
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
4.0 years ago svlachavas • 770 • updated 4.0 years ago Gordon Smyth 41k
1
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1
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6.0k
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Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
4.1 years ago chudar.chudar • 0 • updated 4.1 years ago Michael Love 31k
5
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9
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3.8k
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Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
4.4 years ago komal.rathi • 80
0
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8
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972
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Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
4.4 years ago a.guerra • 0
6
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4
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1.7k
Views
RSEM expected counts to limma-voom
limma voom rsem
4.5 years ago Jake • 70 • updated 4.5 years ago Gordon Smyth 41k
4
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7
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798
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assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
4.6 years ago Assa Yeroslaviz ♦ 1.5k • updated 4.6 years ago James W. MacDonald 55k
1
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3
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1.3k
Views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
4.7 years ago Hugo Varet • 80
41 results • Page 1 of 1
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Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Pedram • 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in by Konstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package by shrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker by Konstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Comment: HTqPCR: dealing with technical replicates (filterCategory) and inability to anal by larissa.stanberry • 0
I ran into the same issue. It appears that filtering does not carry over featureData with the exception of featureNames, e.g. call featureD…
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A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
DEXSeq Usage and Expression Confusion
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