Showing : tximport • reset
4
votes
9
replies
2.3k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ★ 2.0k
0
votes
4
replies
1.4k
views
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
6.8 years ago bruno.saubamea • 0
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
5
votes
6
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3.4k
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 4.6 years ago by ★ 3.3k • written 4.6 years ago by ▴ 80
0
votes
3
replies
1.0k
views
RNA seq tximport
tximport
6.6 years ago tanyabioinfo ▴ 20
2
votes
3
replies
840
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
2
votes
5
replies
1.8k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.3 years ago • updated 2.2 years ago Marianna ▴ 20
3
votes
2
replies
585
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
3
replies
1.3k
views
tximport question on what counts to use for LogFC calculations
tximport
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
7
replies
1.1k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
4.3 years ago • updated 4.2 years ago rafaelsolersanblas ▴ 50
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 15 months ago by 42k • written 15 months ago by ▴ 90
1
vote
3
replies
1.2k
views
Bias correction in single end experiment for DEG and DET
tximport alpine
7.9 years ago yohann.nedelec • 0
0
votes
2
replies
823
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
1
vote
4
replies
862
views
Help with error produced when using makeTxDbFromBiomart
tximport tximport rnaseq
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
6
votes
5
replies
2.3k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.0 years ago hollandademello ▴ 20
3
votes
13
replies
2.4k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
6.3 years ago tim.ivanov.92 • 0
4
votes
5
replies
1.8k
views
GAGE after tximport
gage tximport
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by ▴ 230
2
votes
6
replies
3.0k
views
Subsetting a tximport object
tximport
written 6.2 years ago by • 0
2
votes
7
replies
2.1k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
0
votes
4
replies
1.8k
views
tximport: Error in medianLengthOverIsoform
tximport deseq2 dexseq
5.3 years ago d-joester ▴ 20
0
votes
3
replies
699
views
output of the function "makeCountsFromAbundance"
tximport
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 10
0
votes
4
replies
1.1k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 620
2
votes
8
replies
3.7k
views
Which R version is needed for tximport package?
tximport package R version install tximport
3.7 years ago harelarik ▴ 60
0
votes
2
replies
954
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
2
votes
3
replies
1.5k
views
how to get the lastest version of tximport
tximport stringtie
6.2 years ago • updated 6.0 years ago matrs ▴ 10
32
votes
16
replies
18k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.1 years ago by ▴ 20 • written 7.9 years ago by ▴ 190
2
votes
6
replies
1.6k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
4
votes
3
replies
4.2k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
7.9 years ago jarod_v6@libero.it ▴ 40
5
votes
6
replies
1.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 20 months ago by 50k • written 20 months ago by • 0
1
vote
11
replies
7.2k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
6.6 years ago tanyabioinfo ▴ 20
9
votes
11
replies
5.6k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.2 years ago by ▴ 20 • written 8.1 years ago by ▴ 10
1
vote
5
replies
1.4k
views
Help inputing sailfish TPM files into tximport
tximport sailfish
7.9 years ago sjmonkley ▴ 40
8
votes
12
replies
3.9k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 6.6 years ago by ★ 2.0k • written 6.6 years ago by • 0
3
votes
2
replies
1.6k
views
tximport with versioned identifiers
tximport ensembldb
6.6 years ago Ed Siefker ▴ 230
2
votes
4
replies
1.9k
views
tximport gene name
tximport
updated 6.6 years ago by ▴ 230 • written 6.6 years ago by ▴ 20
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 8 weeks ago by • 0 • written 7.6 years ago by • 0
2
votes
2
replies
2.0k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 50
0
votes
6
replies
2.9k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
7.0 years ago sunil.mangalam • 0
1
vote
3
replies
2.1k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
8.0 years ago Hugo Varet ▴ 80
2
votes
9
replies
1.3k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
3
votes
5
replies
2.4k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 6.6 years ago by • 0 • written 6.9 years ago by ▴ 30
3
votes
4
replies
1.4k
views
tximport and de novo transcriptome
tximport salmon rna seq de novo
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 10
2
votes
3
replies
1.5k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport kallisto
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 40
2
votes
2
replies
1.1k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 6.2 years ago by • 0 • written 6.2 years ago by • 0
6
votes
11
replies
2.1k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
5.0 years ago • updated 4.4 years ago ATpoint ★ 4.1k
2
votes
6
replies
2.4k
views
How to run tximport ?
tximport
updated 3.9 years ago by ★ 4.1k • written 3.9 years ago by • 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.9 years ago keremwai • 0
1
vote
3
replies
859
views
RSEM and Tximport
RSEM tximport deseq2
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
3
votes
3
replies
960
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
19 months ago • updated 18 months ago duhwa.lee • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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