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41 results • Page
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Filtering for tag:
tximport
•
reset
0
votes
4
replies
180
views
Help with salmon quantification of samples with de novo transcriptome
salmon
denovo
tximport
updated 4 days ago by
ponganta
▴ 170 • written 6 days ago by
codyas
• 0
4
votes
10
replies
183
views
Importing quant.sf file to tximport
tximport
tools
genome
software error
27 days ago by
yvarg009
• 0
3
votes
2
replies
2.8k
views
Tximport > DESeq2 (sample names)
DESeq2
tximport
RNA-Seq
updated 4 months ago by
skgtjzw
• 0 • written 2.4 years ago by
Barry Digby
▴ 710
0
votes
4
replies
463
views
Problem with gene names in tximport
tximport
RNA-Seq
rna-seq
R
updated 7 months ago by
Biostar
20 • written 9 months ago by
dioscorea.bulbifera
• 0
1
vote
5
replies
350
views
How to fix extreme outliers not picked up by DESeq2?
DESeq2
RNA-Seq
Outlier
Cook's Distance
TXImport
updated 7 months ago by
antonioggsousa
★ 2.0k • written 7 months ago by
fisher.w.daniel
• 0
1
vote
0
replies
274
views
Import Salmon output by tximport
RNA-Seq
R
tximport
salmon
updated 8 months ago by
Ram
32k • written 8 months ago by
koaeb
▴ 10
0
votes
2
replies
667
views
RSEM isoform.results outputs for edgeR
rsem
tximport
edgeR
9 months ago by
weichengz
• 0
3
votes
3
replies
3.7k
views
Kallisto and downstream analysis with tximport and DESeq2
RNA-Seq
kallisto
tximport
deseq2
10 months ago by
Mozart
▴ 260
3
votes
4
replies
285
views
Tximport Error ... unable to match up my quant.sf and tx2gene columns
RNA-Seq
Tximport
salmon
10 months ago by
2405592M
▴ 100
0
votes
3
replies
431
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq
deseq2
tximport
salmon
10 months ago by
tianshenbio
▴ 90
1
vote
2
replies
527
views
How to subset the output of tximport in DE analysis using DEseq2
DEseq2
tximport
rna-seq
r
10 months ago by
tianshenbio
▴ 90
1
vote
10
replies
787
views
error in TXIMPORT command for RSEM
tximport
rsem
updated 10 months ago by
Kevin Blighe
72k • written 10 months ago by
StartR
▴ 20
1
vote
2
replies
243
views
error in tximport command
tximport
updated 11 months ago by
ATpoint
47k • written 11 months ago by
StartR
▴ 20
2
votes
1
reply
411
views
tximport --> edgeR
tximport
edgeR
RNA-Seq
11 months ago by
u3005992
▴ 20
0
votes
1
reply
909
views
Help with Salmon --> tximport --> edgeR
RNA-Seq
tximport
salmon
edgeR
normalisation
11 months ago by
u3005992
▴ 20
1
vote
5
replies
942
views
How is the bootstrapping information from kallisto treated in DeSeq2 when imported using tximport?
RNA-Seq
kallisto
deseq2
tximport
updated 11 months ago by
ATpoint
47k • written 11 months ago by
divya.nandakumar
▴ 20
0
votes
0
replies
358
views
Issue with Salmon and Deseq2 with paired-end and single-end reads libraries
salmon
deseq2
rnaseq
tximport
14 months ago by
Andrés Ribone
• 0
0
votes
2
replies
1.1k
views
DESeq2 Error: Error: $ operator is invalid for atomic vectors
RNA-Seq
DESeq2
deseq2
tximport
updated 17 months ago by
Biostar
20 • written 18 months ago by
Ulduz
▴ 20
16
votes
4
replies
2.4k
views
Difference between abundance and counts in RNA-Seq
RNA-Seq
tximport
17 months ago by
c_u
▴ 290
1
vote
2
replies
1.7k
views
rna-seq analysis with Salmon - how to Import and summarize using tximport
RNA-Seq
salmon
tximport
19 months ago by
woojoy14
• 0
1
vote
2
replies
2.6k
views
Error in tximport: all(file.exists(files)) is not TRUE
tximport
DESeq2
updated 20 months ago by
h.mon
32k • written 20 months ago by
Farah
▴ 70
0
votes
1
reply
1.3k
views
Tximport for kallisto abundance.tsv files prior to DESeq analysis (RNASeq)
RNA-Seq
rna-seq
R
tximport
20 months ago by
AW
▴ 10
5
votes
9
replies
912
views
How to change my colnames(count.table) as exactly similar to my rownames(meta)?
RNA-Seq
Kallisto
DESeq2
R
tximport
updated 20 months ago by
ATpoint
47k • written 20 months ago by
Farah
▴ 70
1
vote
1
reply
1.1k
views
How to merge Kallisto TSV files for use with Tximport
RNA-Seq
R
Kallisto
Tximport
22 months ago by
Colari19
▴ 50
0
votes
1
reply
2.9k
views
using tximport to prepare salmon quantification files for DEG analysis
RNA-Seq
tximport
updated 2.0 years ago by
Biostar
20 • written 3.0 years ago by
tarek.mohamed
▴ 270
0
votes
1
reply
1.1k
views
how do normalization for transcript length
transcript coverage
plot
salmon
tximport
2.2 years ago by
lkianmehr
▴ 50
0
votes
1
reply
2.2k
views
Error in running DESeqDataSetFromTximport
RNA-Seq
tximport
R
Stringtie
DESeq2
updated 2.4 years ago by
Devon Ryan
98k • written 2.4 years ago by
ankur
• 0
6
votes
4
replies
1.3k
views
Unable to create file for tximport
tximport
StringTie
RNA-Seq
DESeq2
updated 2.4 years ago by
kristoffer.vittingseerup
★ 3.5k • written 2.4 years ago by
ankur
• 0
0
votes
2
replies
1.2k
views
salmon - tximport - deseq2 gene level workflow
RNA-Seq
salmon
deseq2
tximport
2.4 years ago by
jomo018
▴ 610
3
votes
4
replies
1.1k
views
unable to load quant.sf files
R
tximport
2.5 years ago by
shivyasoni1994
• 0
0
votes
2
replies
1.3k
views
RNAseq Tximport transcript counts to gene counts
RNA-Seq
Salmon
Tximport
updated 3.0 years ago by
h.mon
32k • written 3.0 years ago by
s.kyungyong64
▴ 40
1
vote
3
replies
1.1k
views
Differential genes expression in knockdown experiment
Deseq2
Knockout
edgeR
tximport
RSEM
3.2 years ago by
tim.ivanov.92
▴ 20
2
votes
3
replies
2.0k
views
"makeTxDbFromGFF" error ?!
RNA-Seq
tximport
updated 3.4 years ago by
Bastien Hervé
4.9k • written 3.4 years ago by
dina.hesham139
▴ 140
4
votes
9
replies
2.4k
views
Tximport mixing annotations
RNA-Seq
tximport
txdb
3.4 years ago by
Tania
▴ 130
1
vote
2
replies
2.4k
views
Help in tximport
RNAseq
tximport
updated 3.4 years ago by
WouterDeCoster
45k • written 3.4 years ago by
Tania
▴ 130
2
votes
8
replies
2.5k
views
Minimal TPM threshold for qPCR measure of gene expression
qpcr
RNA-Seq
TPM
kallisto
tximport
3.4 years ago by
tlorin
▴ 310
0
votes
4
replies
1.7k
views
edgeR error related to tximport
RNA-Seq
edgeR
tximport
updated 3.4 years ago by
Devon Ryan
98k • written 3.4 years ago by
Sharon
▴ 520
3
votes
3
replies
1.9k
views
Transcripts ID matching in tximport for edgeR
RNA-Seq
edgeR
Salmon
tximport
updated 3.4 years ago by
WouterDeCoster
45k • written 3.4 years ago by
Sharon
▴ 520
2
votes
10
replies
2.1k
views
finding significance between transcripts in a RNA-Seq experiment
tximport
deseq2
edger
limma
kallisto
4.6 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
4.1k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
RNA-Seq
Kallisto
tximport
R
updated 5.0 years ago by
Michael Love
★ 2.2k • written 5.0 years ago by
Sinji
★ 3.1k
11
votes
5
replies
6.3k
views
following Kallisto with DESeq2 using tximport package
deseq2
kallisto
tximport
ucsc
ensembl
updated 5.2 years ago by
Michael Love
★ 2.2k • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
41 results • Page
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Comment: Bioinformatics startup market analysis
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grant.hovhannisyan
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good luck!
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Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
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