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txImport
•
reset
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.0 years ago by
fiona.dick91
▴ 60
2
votes
19
replies
2.7k
views
tximport returns NA counts
tximport
6.4 years ago
leonfodoulian
• 0
2
votes
18
replies
3.4k
views
Using tximport on rsem files produces error while trying to read in files
R
tximport
rnaseq
tpm
rsem
6.1 years ago
stephan.emmrich
▴ 10
7
votes
17
replies
5.4k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2
tximport
7.0 years ago
JWCarlson
▴ 80
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
luxeredias
▴ 20 • written 7.8 years ago by
tangming2005
▴ 190
4
votes
14
replies
2.8k
views
running tximport for salmon quants
tximport
readr
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
Hadi Gharibi
• 0
2
votes
14
replies
1.9k
views
Salmon (quant.sf) to tximport error
tximport
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Merlin
▴ 10
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 months ago by
Michael Love
41k • written 7 months ago by
Christian
• 0
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
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
Johannes Rainer
★ 2.0k • written 6.6 years ago by
prab4th
• 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 5 months ago by
Abhishek
• 0 • written 6 months ago by
RLiu
▴ 40
1
vote
11
replies
7.2k
views
RNA Seq data analysis using Salmon and tximport
RNAseq
tximport
6.5 years ago
tanyabioinfo
▴ 20
2
votes
11
replies
1.8k
views
failure importing data with tximport with error information
software error
tximport
hdf5
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
me5537
▴ 10
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
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
pablo_garcia05
▴ 20 • written 8.0 years ago by
cguzman.bioinformatics
▴ 10
3
votes
11
replies
2.6k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
ty.thomson
▴ 10
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love
Salmon
tximport
tx2gene
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
pvd2107
▴ 30
0
votes
10
replies
2.2k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error
RNAseq
tximport
R
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
ScafioRuo
• 0
5
votes
9
replies
3.4k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
6.2 years ago
emmak
▴ 20
1
vote
9
replies
1.3k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta
tximport
deseq2
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
anthony.nash
▴ 20
4
votes
9
replies
2.2k
views
tximport recommendation for limma-trend downstream analysis?
tximport
limma
limma-trend
edgeR
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
Jenny Drnevich
★ 2.0k
3
votes
9
replies
4.9k
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
5.1 years ago
Leo K
• 0
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
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
Aaron Lun
★ 28k • written 5.9 years ago by
martin.weihrauch
▴ 20
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.8 years ago by
stan
• 0
6
votes
9
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 14 minutes ago by
Michael Love
41k • written 14 months ago by
mohammedtoufiq91
▴ 10
5
votes
9
replies
5.3k
views
Trouble with Tximport
tximport
salmon
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
smithng1215
▴ 30
1
vote
9
replies
2.9k
views
Importing Kallisto counts with tximport
tximport
Kallisto
H5Fopen
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
zroger499
• 0
1
vote
9
replies
2.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR
tximport
rnaseq
salmon
updated 5.0 years ago by
k.vitting.seerup
▴ 120 • written 5.0 years ago by
saddamhusain77
• 0
2
votes
9
replies
1.8k
views
Unused argument of reader = read_tsv on R version 3.4.1
tximport
6.7 years ago
tarun2
• 0
0
votes
8
replies
1.3k
views
tximport question on the values contained in "counts" and "abundance" matrices
tximport
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
HKS
• 0
2
votes
8
replies
732
views
Silent error in tximport after installing GEOquery
tximport
4.6 years ago
penny.lane
• 0
7
votes
8
replies
3.7k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 5.3 years ago by
Bioconductor Community
0 • written 5.4 years ago by
michaelschoeber
▴ 20
0
votes
8
replies
1.9k
views
tximport not working on tsv files
tximport
4.7 years ago
HKS
• 0
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
22 months ago • updated 21 months ago
Kelen
▴ 10
0
votes
8
replies
1.8k
views
Importing RSEM with tximport
tximport
RSEM
import error
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
harelarik
▴ 60
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
8
replies
2.5k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2
tximport
rsem
saimon
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
LD
• 0
1
vote
8
replies
2.8k
views
IgnoreTxVersion on Tximport not working
Tximport
Salmon
4.6 years ago
k1m
▴ 20
2
votes
7
replies
2.6k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon
hg38
tximport
tx2gene.csv
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
seb.boegel
• 0
2
votes
7
replies
2.0k
views
RNA-seq with Salmon and tximport
RNA-seq
Salmon
tximport
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
woojoy14
• 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
11 months ago
Yijing
• 0
2
votes
7
replies
2.0k
views
Obtaining transcript names in RSEM
tximport
rsem
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
deena
▴ 20
1
vote
7
replies
2.1k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport
limma
rnaseq
updated 3.1 years ago by
Aubrey
• 0 • written 3.9 years ago by
Ahdee
▴ 50
1
vote
7
replies
1.9k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2
tximport
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
rensanhao
• 0
4
votes
7
replies
3.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2
tximport
tcga
rsem
firebrowse
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
J. Smith
• 0
0
votes
7
replies
1.7k
views
Problem with Tximport
tximportData
tximport
3.2 years ago
agoesmartini
• 0
0
votes
7
replies
2.4k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 2.5 years ago by
nicolette.sipperly
• 0 • written 6.9 years ago by
urjaswita
▴ 40
2
votes
7
replies
2.1k
views
Get the countsFromAbundance as limma input
tximport
limma
deseq2
differential expression
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
mico
• 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
50 results • Page
1 of 1
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Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
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