Showing : Tximport • reset
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.6 years ago by ▴ 20 • written 8.4 years ago by ▴ 200
16
votes
25
replies
3.7k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.7 years ago by ▴ 60
10
votes
11
replies
2.7k
views
tximport error: vroom
tximport
updated 13 months ago by • 0 • written 14 months ago by ▴ 40
9
votes
2
replies
9.8k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 3.3 years ago by 43k • written 7.8 years ago by ▴ 10
9
votes
4
replies
3.9k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 30
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.8 years ago by ▴ 20 • written 8.7 years ago by ▴ 10
8
votes
12
replies
4.3k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 7.2 years ago by ★ 2.1k • written 7.2 years ago by • 0
7
votes
17
replies
6.0k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
7.6 years ago JWCarlson ▴ 80
7
votes
8
replies
4.4k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 5.9 years ago by 0 • written 6.1 years ago by ▴ 20
6
votes
5
replies
2.9k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.6 years ago hollandademello ▴ 20
6
votes
6
replies
2.6k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.0 years ago svlachavas ▴ 840
6
votes
11
replies
2.5k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
5.6 years ago • updated 4.9 years ago ATpoint ★ 4.6k
6
votes
10
replies
2.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 months ago by • 0 • written 22 months ago by ▴ 10
6
votes
4
replies
3.3k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.7 years ago Al90 ▴ 10
6
votes
4
replies
5.2k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
6
votes
2
replies
1.3k
views
tximport + edgeR not recommended?
tximport edgeR
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
5
votes
5
replies
5.5k
views
tximport transcript missing
deseq2 salmon tximport
5.4 years ago mr6518849 ▴ 10
5
votes
3
replies
3.4k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 40
5
votes
9
replies
3.9k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.9 years ago emmak ▴ 20
5
votes
6
replies
4.1k
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 5.2 years ago by ★ 3.4k • written 5.2 years ago by ▴ 80
5
votes
5
replies
3.3k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 8.2 years ago by 43k • written 8.2 years ago by ★ 2.0k
5
votes
6
replies
1.9k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
5
votes
2
replies
1.8k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
5
votes
9
replies
5.9k
views
Trouble with Tximport
tximport salmon
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 30
5
votes
10
replies
12k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
4
votes
3
replies
4.4k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
8.5 years ago jarod_v6@libero.it ▴ 40
4
votes
6
replies
2.5k
views
Using spike-in RNA for normalization of Salmon counts imported using Tximport
deseq2 Tximport Sizefactors normalizationfactors spike-in
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
4
votes
9
replies
2.6k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ★ 2.0k
4
votes
14
replies
3.1k
views
running tximport for salmon quants
tximport readr
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
4
votes
7
replies
4.7k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
4
votes
3
replies
3.7k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 3.0 years ago by • 0 • written 7.4 years ago by • 0
4
votes
3
replies
1.7k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 3.5 years ago by 43k • written 3.6 years ago by ▴ 40
4
votes
9
replies
4.9k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 18 months ago by • 0 • written 7.5 years ago by • 0
4
votes
5
replies
609
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
5 weeks ago LuciaNhu • 0
4
votes
1
reply
1.3k
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 20
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 10
4
votes
3
replies
1.9k
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
6.7 years ago pvd2107 ▴ 30
4
votes
5
replies
2.0k
views
GAGE after tximport
gage tximport
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by ▴ 230
4
votes
13
replies
2.6k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
4
votes
3
replies
1.2k
views
Trouble with Tximport for edgeR
tximport edger
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
4
votes
3
replies
2.1k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
4.6 years ago zroger499 • 0
3
votes
2
replies
1.7k
views
tximport with versioned identifiers
tximport ensembldb
7.1 years ago Ed Siefker ▴ 230
3
votes
5
replies
2.9k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 3.9 years ago by 67k • written 7.8 years ago by • 0
3
votes
1
reply
1.2k
views
tximport rowsum error
tximport
3.8 years ago Ezgi ▴ 60
3
votes
1
reply
2.9k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 8.5 years ago by 43k • written 8.5 years ago by ★ 13k
3
votes
3
replies
1.6k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
3
votes
11
replies
2.9k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
3
votes
2
replies
7.2k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 8.1 years ago by 43k • written 8.1 years ago by ★ 2.0k
3
votes
5
replies
2.6k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 7.2 years ago by • 0 • written 7.5 years ago by ▴ 30
3
votes
4
replies
4.2k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Comment: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Comment: Help using rtracklayer for gene ID extraction by Aichatou • 0
Hello, Please disregard the previous post. it's working now, i think. I am able to create the txdb object but I can't see all the other inf…
Comment: p value is 0, padj is 0 by Wirayatida • 0
Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.
Comment: p value is 0, padj is 0 by Wirayatida • 0
Thank you so much for your information. I understand it.
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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