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txImport
•
reset
0
votes
4
replies
1.0k
views
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2
salmon
tximport
4.9 years ago
bruno.saubamea
• 0
5
votes
6
replies
1.6k
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 2.7 years ago by
Robert Castelo
★ 2.9k • written 2.7 years ago by
Stephanie Hicks
▴ 80
0
votes
3
replies
631
views
RNA seq tximport
tximport
4.7 years ago
tanyabioinfo
▴ 20
4
votes
9
replies
1.3k
views
tximport recommendation for limma-trend downstream analysis?
tximport
limma
limma-trend
edgeR
updated 4.8 years ago by
Aaron Lun
★ 27k • written 4.8 years ago by
Jenny Drnevich
★ 2.0k
2
votes
2
replies
439
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
2.0 years ago
keremwai
• 0
2
votes
3
replies
850
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport
kallisto
updated 3.5 years ago by
Gordon Smyth
45k • written 3.5 years ago by
Lucas Carey
▴ 40
3
votes
4
replies
839
views
tximport and de novo transcriptome
tximport
salmon rna seq
de novo
updated 3.8 years ago by
James W. MacDonald
60k • written 3.8 years ago by
RMRG
▴ 10
1
vote
4
replies
518
views
Help with error produced when using makeTxDbFromBiomart
tximport
tximport rnaseq
updated 3.8 years ago by
James W. MacDonald
60k • written 3.8 years ago by
pat20
• 0
3
votes
5
replies
558
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR
tximport
differential expression
2.1 years ago
hollandademello
• 0
0
votes
7
replies
386
views
tximeta doesn't work downloading the ref genome
deseq2
tximeta
tximport
rnaseq
2.4 years ago
rafaelsolersanblas
▴ 50
0
votes
2
replies
365
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon
EnsDb.Hsapiens.v86
tximport
updated 17 months ago by
James W. MacDonald
60k • written 17 months ago by
TJ
• 0
2
votes
5
replies
340
views
from kallisto to deseq2 analysis
biomaRt
DESeq2
tximport
4 months ago
Marianna
• 0
2
votes
6
replies
1.1k
views
How to run tximport ?
tximport
updated 2.0 years ago by
ATpoint
★ 1.3k • written 2.0 years ago by
sunnykevin97
• 0
4
votes
3
replies
3.7k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport
deseq2
6.0 years ago
jarod_v6@libero.it
▴ 40
4
votes
5
replies
1.0k
views
GAGE after tximport
gage
tximport
updated 4.7 years ago by
Luo Weijun
★ 1.5k • written 4.7 years ago by
Ed Siefker
▴ 230
2
votes
3
replies
903
views
how to get the lastest version of tximport
tximport
stringtie
4.4 years ago • updated 4.1 years ago
matrs
▴ 10
1
vote
11
replies
5.6k
views
RNA Seq data analysis using Salmon and tximport
RNAseq
tximport
4.8 years ago
tanyabioinfo
▴ 20
3
votes
13
replies
1.2k
views
tximport's parameter for countsFromAbundance doesn't work
tximport
rsem
edger
4.4 years ago
tim.ivanov.92
• 0
2
votes
6
replies
1.7k
views
Subsetting a tximport object
tximport
updated 4.3 years ago by
jennietodd141
• 0 • written 4.3 years ago by
scanchi
• 0
2
votes
7
replies
1.0k
views
Get the countsFromAbundance as limma input
tximport
limma
deseq2
differential expression
updated 3.8 years ago by
Gordon Smyth
45k • written 3.8 years ago by
mico
• 0
0
votes
4
replies
971
views
tximport: Error in medianLengthOverIsoform
tximport
deseq2
dexseq
3.4 years ago
d-joester
▴ 20
0
votes
3
replies
392
views
output of the function "makeCountsFromAbundance"
tximport
updated 3.2 years ago by
James W. MacDonald
60k • written 3.2 years ago by
capricygcapricyg
• 0
0
votes
4
replies
397
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport
isoform
voom
updated 24 months ago by
Gordon Smyth
45k • written 24 months ago by
Ina Hoeschele
▴ 620
2
votes
8
replies
1.7k
views
Which R version is needed for tximport package?
tximport
package
R version
install tximport
22 months ago
harelarik
▴ 50
9
votes
11
replies
4.6k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport
Kallisto
rna-seq
updated 5.4 years ago by
pablo_garcia05
▴ 20 • written 6.2 years ago by
cguzman.bioinformatics
▴ 10
0
votes
3
replies
433
views
tximport question on what counts to use for LogFC calculations
tximport
updated 7 months ago by
Michael Love
37k • written 7 months ago by
mailmpunta
• 0
1
vote
3
replies
847
views
Bias correction in single end experiment for DEG and DET
tximport
alpine
6.0 years ago
yohann.nedelec
• 0
2
votes
6
replies
912
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 4.1 years ago by
Michael Love
37k • written 4.1 years ago by
changhan1110
• 0
1
vote
5
replies
994
views
Help inputing sailfish TPM files into tximport
tximport
sailfish
6.0 years ago
sjmonkley
▴ 30
5
votes
11
replies
1.0k
views
Correct use of tximport in combination with edgeR cpm()
tximport
edgeR
3.1 years ago • updated 2.5 years ago
ATpoint
★ 1.3k
8
votes
12
replies
2.5k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport
deseq2
annotationdbi
updated 4.8 years ago by
Johannes Rainer
★ 2.0k • written 4.8 years ago by
prab4th
• 0
2
votes
2
replies
575
views
tximport failing at importing TPM instead of FPKM
tximport
rnaseq
rsem
updated 4.4 years ago by
rosabellascottgm
• 0 • written 4.4 years ago by
fresard.laure
• 0
28
votes
16
replies
13k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 4.2 years ago by
luxeredias
▴ 10 • written 6.0 years ago by
tangming2005
▴ 190
1
vote
3
replies
331
views
RSEM and Tximport
RSEM
tximport
deseq2
updated 2.1 years ago by
James W. MacDonald
60k • written 2.1 years ago by
pthom010
• 0
3
votes
2
replies
929
views
tximport with versioned identifiers
tximport
ensembldb
4.7 years ago
Ed Siefker
▴ 230
2
votes
4
replies
1.0k
views
tximport gene name
tximport
updated 4.7 years ago by
Ed Siefker
▴ 230 • written 4.7 years ago by
tanyabioinfo
▴ 20
0
votes
4
replies
5.9k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
5.8 years ago
ctl
• 0
2
votes
2
replies
1.2k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport
limma
rna-seq
updated 4.6 years ago by
Michael Love
37k • written 4.6 years ago by
Ahdee
▴ 50
0
votes
6
replies
2.4k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport
DESeq2
"tximport"
deseq2
salmon
5.1 years ago
sunil.mangalam
• 0
1
vote
3
replies
1.5k
views
DESeq2 size factors estimation after RSEM quantification
deseq2
tximport
rsem
estimatesizefactors
6.2 years ago
Hugo Varet
▴ 80
2
votes
9
replies
778
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon
edger
tximport
rnaseq
updated 4.1 years ago by
Aaron Lun
★ 27k • written 4.1 years ago by
martin.weihrauch
▴ 10
3
votes
5
replies
1.8k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2
tximport
updated 4.8 years ago by
Ming Wang
• 0 • written 5.1 years ago by
ben
▴ 30
2
votes
7
replies
1.9k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon
hg38
tximport
tx2gene.csv
updated 5.3 years ago by
Michael Love
37k • written 5.3 years ago by
seb.boegel
• 0
0
votes
1
reply
512
views
how to deal with the cufflinks files
tximport
updated 5.0 years ago by
Michael Love
37k • written 5.0 years ago by
xiaoaozqd
• 0
3
votes
5
replies
2.0k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 17 months ago by
James W. MacDonald
60k • written 5.3 years ago by
alexlok
• 0
7
votes
4
replies
2.5k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 5.3 years ago by
Michael Love
37k • written 5.3 years ago by
dmr210
▴ 20
6
votes
2
replies
5.5k
views
Using RSEM with tximport and DESeq2
deseq2
tximport
software error
bug
updated 10 months ago by
Michael Love
37k • written 5.4 years ago by
falkohofmann
• 0
0
votes
1
reply
1.2k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 5.4 years ago by
Michael Love
37k • written 5.4 years ago by
Peter Alto
▴ 10
3
votes
1
reply
2.3k
views
Gene level exploratory data analysis from tximport results
tximport
edgeR
DESeq2
updated 6.0 years ago by
Michael Love
37k • written 6.0 years ago by
Steve Lianoglou
13k
0
votes
4
replies
909
views
tximport RSEM error
tximport
updated 5.5 years ago by
Michael Love
37k • written 5.5 years ago by
ribioinfo
▴ 100
50 results • Page
1 of 1
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Comment: Seeking help in multifactor differential gene expression analysis using DESeq2.
by
ac.mainul.mmb
• 0
Thanks for your kind reply. Those genes belong to HSP20, Suppose to have high expression under HT but if we look into the table its has hig…
Answer: Seeking help in multifactor differential gene expression analysis using DESeq2.
by
swbarnes2
★ 1.1k
Those look like different results to me. It's not at all clear why you are so sure it's wrong. Have you eyeballed to expression of those …
Answer: bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
by
Malcolm Cook
★ 1.6k
You have many more packages loaded than needed for a minimal example. I bet will work in a new session since your example works in my han…
Comment: treeio installation problem
by
an.gorohovski
• 0
Get the released version from Bioconductor: ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly…
Comment: cellCounts() function floating point error
by
J-E
• 0
Thanks for your patience. There was an object 'cellCounts' in my workspace that was masking the most updated function from Rsubread 2.10.4.…
Votes
Answer: How fix lines of dendrogram that overlap in the column portion of a heatmap?
how do singleton samples contribute to dispersion estimate in DESeq2?
Answer: Combine GRanges(List) to a single GRanges with unified breakpoints
Answer: Combine GRanges(List) to a single GRanges with unified breakpoints
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
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