Showing : Tximport • reset
4
votes
9
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2.2k
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
6.7 years ago bruno.saubamea • 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 6 months ago by 41k • written 7 months ago by • 0
5
votes
6
replies
3.3k
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 4.5 years ago by ★ 3.2k • written 4.5 years ago by ▴ 80
0
votes
3
replies
1.0k
views
RNA seq tximport
tximport
6.5 years ago tanyabioinfo ▴ 20
2
votes
3
replies
784
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
2
votes
5
replies
1.7k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.2 years ago Marianna ▴ 20
3
votes
2
replies
539
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
0
votes
3
replies
1.2k
views
tximport question on what counts to use for LogFC calculations
tximport
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
0
votes
7
replies
1.1k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
4.2 years ago rafaelsolersanblas ▴ 50
2
votes
9
replies
1.1k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
1
vote
5
replies
1.1k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 14 months ago by 41k • written 14 months ago by ▴ 90
1
vote
3
replies
1.2k
views
Bias correction in single end experiment for DEG and DET
tximport alpine
7.8 years ago yohann.nedelec • 0
0
votes
2
replies
764
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 15 months ago by • 0
1
vote
4
replies
843
views
Help with error produced when using makeTxDbFromBiomart
tximport tximport rnaseq
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
6
votes
5
replies
2.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
3.9 years ago hollandademello ▴ 20
3
votes
13
replies
2.4k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
6.2 years ago tim.ivanov.92 • 0
4
votes
5
replies
1.7k
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
2.9k
views
Subsetting a tximport object
tximport
written 6.1 years ago by • 0
2
votes
7
replies
2.1k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
0
votes
4
replies
1.7k
views
tximport: Error in medianLengthOverIsoform
tximport deseq2 dexseq
5.2 years ago d-joester ▴ 20
0
votes
3
replies
678
views
output of the function "makeCountsFromAbundance"
tximport
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
4
replies
1.0k
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
3.6k
views
Which R version is needed for tximport package?
tximport package R version install tximport
3.6 years ago harelarik ▴ 60
0
votes
2
replies
931
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.2 years ago by 65k • written 3.2 years ago by • 0
2
votes
3
replies
1.5k
views
how to get the lastest version of tximport
tximport stringtie
6.1 years ago • updated 5.9 years ago matrs ▴ 10
32
votes
16
replies
17k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.0 years ago by ▴ 20 • written 7.8 years ago by ▴ 190
2
votes
6
replies
1.6k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
4
votes
3
replies
4.2k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
7.8 years ago jarod_v6@libero.it ▴ 40
5
votes
6
replies
1.4k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 19 months ago by 50k • written 19 months ago by • 0
1
vote
11
replies
7.2k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
6.5 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 8.0 years ago by ▴ 10
1
vote
5
replies
1.4k
views
Help inputing sailfish TPM files into tximport
tximport sailfish
7.8 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
6.5 years ago Ed Siefker ▴ 230
2
votes
4
replies
1.9k
views
tximport gene name
tximport
updated 6.5 years ago by ▴ 230 • written 6.5 years ago by ▴ 20
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 4 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 6.4 years ago by 41k • written 6.4 years ago by ▴ 50
0
votes
6
replies
2.8k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
6.9 years ago sunil.mangalam • 0
1
vote
3
replies
2.1k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
7.9 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 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
3
votes
5
replies
2.4k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 6.5 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 5.3 years ago by 50k • written 5.3 years ago by ▴ 40
2
votes
2
replies
1.0k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 6.1 years ago by • 0 • written 6.1 years ago by • 0
6
votes
11
replies
2.1k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
4.9 years ago • updated 4.3 years ago ATpoint ★ 4.0k
2
votes
6
replies
2.4k
views
How to run tximport ?
tximport
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.8 years ago keremwai • 0
1
vote
3
replies
829
views
RSEM and Tximport
RSEM tximport deseq2
updated 3.8 years ago by 65k • written 3.8 years ago by • 0
3
votes
3
replies
898
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
18 months ago • updated 17 months ago duhwa.lee • 0
50 results • Page 1 of 1
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Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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