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Showing :
txImport
•
reset
2
votes
8
replies
251
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
13 days ago • updated 2 days ago
Kelen
• 0
0
votes
4
replies
90
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
6 days ago
uhlkatie
• 0
1
vote
3
replies
260
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 11 days ago by
Michael Love
37k • written 16 days ago by
BG
• 0
0
votes
1
reply
132
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 6 weeks ago by
ATpoint
★ 1.3k • written 6 weeks ago by
johnmcma
▴ 10
0
votes
1
reply
122
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport
R
updated 7 weeks ago by
Michael Love
37k • written 8 weeks ago by
cthangav
• 0
2
votes
3
replies
212
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
9 weeks ago
Maka
• 0
2
votes
4
replies
218
views
confused with tximport counts abundance using salmon input
RNASeq
tximport
12 weeks ago
Al90
• 0
0
votes
2
replies
311
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux
R
tximport
4 months ago
nakane_clan
• 0
2
votes
5
replies
342
views
from kallisto to deseq2 analysis
biomaRt
DESeq2
tximport
4 months ago
Marianna
• 0
2
votes
3
replies
265
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 4 months ago by
Michael Love
37k • written 4 months ago by
Luisa
• 0
0
votes
1
reply
175
views
tximport
salmon
tximport
updated 5 months ago by
Michael Love
37k • written 5 months ago by
Pragathi
• 0
0
votes
1
reply
208
views
Ensembl dataset version
tximport
rna
rnaseqGene
biomaRt
updated 6 months ago by
ATpoint
★ 1.3k • written 6 months ago by
st3472
• 0
4
votes
3
replies
2.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport
salmon
R
bioconductor
updated 6 months ago by
Ming Wang
• 0 • written 5.0 years ago by
macmanes
• 0
1
vote
4
replies
636
views
tximport from Galaxy output
normalization
tximport
updated 7 months ago by
Pragathi
• 0 • written 3.0 years ago by
agustin.gonvi
▴ 10
0
votes
3
replies
436
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
0
votes
4
replies
534
views
Filtering output from tximport
tximport
Salmon
updated 7 months ago by
Michael Love
37k • written 7 months ago by
Sheean
• 0
1
vote
3
replies
663
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
8 months ago • updated 7 months ago
nicolette.sipperly
• 0
0
votes
3
replies
352
views
tximport cannot inport RSEM FPKM data
tximport
updated 7 months ago by
Michael Love
37k • written 2.0 years ago by
137737756
• 0
0
votes
1
reply
480
views
tximport samples with separate tx2gene maps
tximport
updated 8 months ago by
Michael Love
37k • written 8 months ago by
nicolette.sipperly
• 0
0
votes
7
replies
1.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 8 months ago by
nicolette.sipperly
• 0 • written 5.1 years ago by
urjaswita
▴ 40
2
votes
1
reply
304
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 8 months ago by
Michael Love
37k • written 8 months ago by
BioNovice247
• 0
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
2
replies
412
views
Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon
ignoreTxVersion
tximport
updated 10 months ago by
Michael Love
37k • written 10 months ago by
robeaumont
• 0
1
vote
2
replies
329
views
tximeta countsFromAbundance for downstream analysis
tximeta
tximport
11 months ago
paulimer
• 0
2
votes
3
replies
438
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 12 months ago by
James W. MacDonald
60k • written 12 months ago by
luca.s
▴ 10
25 results • Page
1 of 1
Recent ...
Replies
Comment: Why Negative value from GSVA
by
Yang Shi
• 0
Thanks for your detailed reply sir! Sorry for the typo 'Row'. Actually, the raw count data is from TCGA database (STAR - Count). The Log2(F…
Comment: ComplexHeatmap - Heatmap function within a for loop
by
krushnach80
• 0
I'm trying to save list of heatmaps after doing this hm_lst<-cmplx_ht(list_of_files,metadata) The to save I tried something like thi…
Answer: calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMet
by
James W. MacDonald
60k
When a function is deprecated, that usually doesn't mean that the author/maintainer just changed the name of a function. That's always poss…
Answer: Cannot Install WGCNA
by
shepherl
3.1k
If you first install preprocessCore and then try again? `BiocManager::install("preprocessCore")` `BiocManager::install("WGCNA")` …
Answer: Why Negative value from GSVA
by
Robert Castelo
★ 2.9k
hi, i guess when you say that you are using "RNA-Seq Row Count data" you mean "RNA-Seq raw count data" in the sense that the count data is …
Votes
Answer: Why Negative value from GSVA
Mapping patient dataset onto control dataset
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
Answer: Error message: Could not find function "DESeqDataSetFromMatrix"
XVector installation fails because zlib.h is not found
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