Showing : txImport • reset
30
votes
16
replies
13k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 4.3 years ago by ▴ 20 • written 6.1 years ago by ▴ 190
9
votes
11
replies
4.7k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 5.5 years ago by ▴ 20 • written 6.3 years ago by ▴ 10
8
votes
12
replies
2.6k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 4.9 years ago by ★ 2.0k • written 4.9 years ago by • 0
7
votes
8
replies
2.3k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 3.6 years ago by 0 • written 3.7 years ago by ▴ 20
7
votes
17
replies
4.3k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
5.3 years ago JWCarlson ▴ 80
7
votes
4
replies
2.6k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 5.5 years ago by 37k • written 5.5 years ago by ▴ 20
6
votes
6
replies
1.1k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
20 months ago svlachavas ▴ 800
6
votes
2
replies
5.7k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 11 months ago by 37k • written 5.5 years ago by • 0
6
votes
2
replies
536
views
tximport + edgeR not recommended?
tximport edgeR
updated 2.1 years ago by 37k • written 2.1 years ago by • 0
6
votes
4
replies
3.7k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 5.4 years ago by 7.8k • written 5.4 years ago by ▴ 10
5
votes
10
replies
7.2k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 4.5 years ago by 37k • written 4.5 years ago by ▴ 30
5
votes
3
replies
1.7k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 2.1 years ago by 37k • written 2.1 years ago by ▴ 40
5
votes
9
replies
2.2k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
4.5 years ago emmak ▴ 20
5
votes
11
replies
1.1k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
3.3 years ago • updated 2.6 years ago ATpoint ★ 1.4k
5
votes
6
replies
1.7k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta ensembldb single-cell snRNA-seq tximport
updated 2.8 years ago by ★ 2.9k • written 2.9 years ago by ▴ 80
5
votes
5
replies
2.1k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 5.9 years ago by 37k • written 5.9 years ago by ★ 2.0k
5
votes
9
replies
3.9k
views
Trouble with Tximport
tximport salmon
updated 6.3 years ago by 37k • written 6.3 years ago by ▴ 30
5
votes
5
replies
2.8k
views
tximport transcript missing
deseq2 salmon tximport
3.1 years ago mr6518849 ▴ 10
4
votes
3
replies
3.7k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
6.1 years ago jarod_v6@libero.it ▴ 40
4
votes
3
replies
551
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 14 months ago by 37k • written 14 months ago by ▴ 30
4
votes
3
replies
1.1k
views
Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2 tximport org.mm.eg.db gencode
4.4 years ago pvd2107 ▴ 30
4
votes
14
replies
2.1k
views
running tximport for salmon quants
tximport readr
updated 6.2 years ago by 37k • written 6.2 years ago by • 0
4
votes
9
replies
1.4k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ★ 2.0k
4
votes
7
replies
1.6k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 2.3 years ago by 3.6k • written 2.3 years ago by • 0
4
votes
5
replies
1.1k
views
GAGE after tximport
gage tximport
updated 4.8 years ago by ★ 1.5k • written 4.8 years ago by ▴ 230
4
votes
3
replies
2.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 7 months ago by • 0 • written 5.1 years ago by • 0
4
votes
7
replies
2.9k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 5.1 years ago by 37k • written 5.1 years ago by • 0
4
votes
3
replies
669
views
Trouble with Tximport for edgeR
tximport edger
updated 4.5 years ago by 46k • written 4.5 years ago by • 0
4
votes
1
reply
730
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 3.3 years ago by 37k • written 3.3 years ago by ▴ 20
3
votes
2
replies
960
views
tximport with versioned identifiers
tximport ensembldb
4.8 years ago Ed Siefker ▴ 230
3
votes
5
replies
2.0k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 19 months ago by 60k • written 5.5 years ago by • 0
3
votes
1
reply
2.3k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 6.2 years ago by 37k • written 6.2 years ago by 13k
3
votes
3
replies
894
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 4.9 years ago by 37k • written 4.9 years ago by ▴ 20
3
votes
11
replies
1.8k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 6.2 years ago by 37k • written 6.2 years ago by ▴ 10
3
votes
2
replies
5.1k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 5.8 years ago by 37k • written 5.8 years ago by ★ 2.0k
3
votes
1
reply
289
views
Can tximport be used to mitigate sample specific length biases?
RNASeq tximport
updated 2.7 years ago by 37k • written 2.7 years ago by ▴ 30
3
votes
4
replies
2.3k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 4.7 years ago by 37k • written 4.7 years ago by ▴ 10
3
votes
13
replies
1.3k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
4.5 years ago tim.ivanov.92 • 0
3
votes
3
replies
486
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
2.3 years ago zroger499 • 0
3
votes
4
replies
730
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 3.4 years ago by 37k • written 3.4 years ago by ▴ 10
3
votes
2
replies
792
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 3.7 years ago by 60k • written 3.7 years ago by • 0
3
votes
5
replies
1.8k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 4.9 years ago by • 0 • written 5.2 years ago by ▴ 30
3
votes
9
replies
2.6k
views
txi <- tximport(files, type="salmon", tx2gene=tx2gene) Error in tximport(files, type = "salmon", tx2gene = tx2gene) : all(file.exists(files)) is n…
deseq2 tximport file.path files file.exists
3.5 years ago • updated 3.4 years ago Leo K • 0
3
votes
1
reply
779
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 3.3 years ago by 37k • written 3.3 years ago by ▴ 20
3
votes
4
replies
859
views
tximport and de novo transcriptome
tximport salmon rna seq de novo
updated 3.9 years ago by 60k • written 3.9 years ago by ▴ 10
3
votes
5
replies
604
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
2.3 years ago • updated 2.2 years ago hollandademello • 0
2
votes
7
replies
2.0k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 5.4 years ago by 37k • written 5.4 years ago by • 0
2
votes
6
replies
939
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 4.2 years ago by 37k • written 4.2 years ago by • 0
2
votes
6
replies
1.2k
views
Can Tximport average transcript length be used for GOSeq?
deseq2 tximport goseq
4.4 years ago casey.rimland ▴ 150
2
votes
2
replies
601
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
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Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
It's relevant for me, thank you for the information!
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
Thank you for sharing!
Comment: conditional command within GRanges by Basti ▴ 390
I can't reproduce your issue because you did not provided an example of your dataset (example with `dput(head(data1))`, but in the first ca…
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
That sounds like you have the wrong version of the annotation compared to which version you used for the quantification?
Comment: Error in Create switchAnalyzeRlist by bpshtiwan ▴ 10
Great... now it is same. but still I have problem with four possibilities during using IsoformSwitchAnalyzeR. Knidly, any idea where is the…
Votes
Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
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