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50 results • Page
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Showing top results for tag:
tximport
•
reset
3
votes
8
replies
876
views
Kallisto: to scaledTPM or not to scaledTPM
tximport
kallisto
EdgeR
RNAseq
updated 16 days ago by
Gordon Smyth
★ 7.4k • written 20 days ago by
IM
• 0
0
votes
1
reply
412
views
How to extract gene_counts_length_scaled matrix from either raw count matrix or SE object
recount3
salmon
gtex
tximport
deseq2
updated 3 months ago by
ATpoint
84k • written 3 months ago by
Aditya
• 0
0
votes
0
replies
213
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 6 months ago by
Ram
44k • written 6 months ago by
PK
▴ 130
0
votes
4
replies
566
views
isoformSwithAnalyzeR importRdata error
tximport
h5
isoformSwitchAnalyzeR
kallisto
updated 8 months ago by
i.sudbery
20k • written 8 months ago by
bsmith030465
▴ 240
3
votes
4
replies
1.1k
views
Getting gene counts from transcript counts using R package 'tximport'
tximport
RNA-seq
updated 9 months ago by
Ram
44k • written 9 months ago by
arsala521
▴ 50
2
votes
3
replies
869
views
tximport error: vroom
tximport
12 months ago by
Maxine
▴ 50
1
vote
4
replies
915
views
How to assign gene names after kallisto when I add GFP?
tximport
RNA-seq
kallisto
11 months ago by
bioinfo
▴ 150
1
vote
22
replies
2.5k
views
error with Tximport when txOut = TRUE
tximport
R
updated 14 months ago by
Ram
44k • written 14 months ago by
mbansal
• 0
4
votes
12
replies
1.7k
views
Can I use abundance from Tximport to compare the expression level of transcript in same condition?
Salmon
Tximport
updated 18 months ago by
Ram
44k • written 18 months ago by
aimanbarki
▴ 20
2
votes
5
replies
1.3k
views
Problem with tximport and plasmodium falciparum
tximport
19 months ago by
bioinfo
▴ 150
0
votes
1
reply
497
views
How do I use tximport to annotate using ensemble annotation on GRCh37.75?
tximport
ensemble
annotation
updated 19 months ago by
ATpoint
84k • written 19 months ago by
biotrekker
▴ 100
2
votes
3
replies
1.2k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
tximport
deseq2
RNA-seq
updated 20 months ago by
Ram
44k • written 20 months ago by
Hicham
▴ 10
0
votes
2
replies
912
views
Normalizing Salmon output count data matrix using DESeq2
tximport
counts
Salmon
DESeq2
updated 21 months ago by
ATpoint
84k • written 21 months ago by
singcell
• 0
5
votes
7
replies
1.6k
views
Extreme shrinkage in DESeq2
salmon
shrinkage
tximport
DESeq2
updated 21 months ago by
ATpoint
84k • written 21 months ago by
DCZ
▴ 10
2
votes
1
reply
1.3k
views
Question about length values given by salmon and tximport
salmon
tximport
RNA-seq
updated 21 months ago by
Ram
44k • written 21 months ago by
Josh
▴ 20
0
votes
1
reply
1.2k
views
Import quant.sf files
tximport
RNAseq
tximeta
updated 21 months ago by
ATpoint
84k • written 21 months ago by
Andrea
▴ 10
1
vote
4
replies
1.3k
views
How to convert transcript counts to gene counts
tximport
r
gene_counts
RNAseq
updated 23 months ago by
manaswwm
▴ 530 • written 23 months ago by
LDT
▴ 340
0
votes
0
replies
454
views
transcripts missing from tx2gene
tximport
updated 2.0 years ago by
ATpoint
84k • written 2.0 years ago by
Erick
• 0
0
votes
0
replies
422
views
How do I get estimated gene counts for a reference that contains GFP using Kallisto?
gene
ensembl
tximport
kallisto
2.0 years ago by
bioinfo
▴ 150
0
votes
1
reply
725
views
Best way to make a PCA plot integrating in-house data with public data?
tximport
SRA
RNA-seq
plot
PCA
updated 2.1 years ago by
Hamid Ghaedi
3.2k • written 2.1 years ago by
Trivas
★ 1.8k
0
votes
0
replies
497
views
TxImport for Transcript to Gene Level Conversion of RNA files
tximport
R
RNA
2.4 years ago by
cthangav
▴ 110
0
votes
2
replies
1.1k
views
How exactly count numbers are calculated with tximport
tximport
kallisto
bioconductor
updated 2.5 years ago by
ATpoint
84k • written 2.5 years ago by
jenabris
• 0
0
votes
6
replies
1.0k
views
Stringtie assembling and quantifying using multiple datasets with various read lengths
Tximport
Stringtie
2.6 years ago by
dadrasarmin
▴ 20
0
votes
1
reply
524
views
tximport
tximport
updated 2.6 years ago by
rpolicastro
13k • written 2.6 years ago by
Saheed
• 0
5
votes
4
replies
3.0k
views
How to subset the output of tximport in DE analysis using DEseq2
DEseq2
tximport
rna-seq
r
updated 2.7 years ago by
ATpoint
84k • written 4.3 years ago by
tianshenbio
▴ 180
4
votes
2
replies
1.0k
views
Estimated gene counts with tximport
RNA-seq
ensembl
tximport
kallisto
updated 2.3 years ago by
Ram
44k • written 2.7 years ago by
bioinfo
▴ 150
1
vote
3
replies
3.5k
views
Import Salmon outputs into DESeq2
into
outputs
DESeq2
Import
tximport
using
Salmon
2.7 years ago by
kimmitzka
• 0
0
votes
2
replies
1.3k
views
Tximport in usegalaxy
tximport
updated 2.8 years ago by
antonioggsousa
3.2k • written 2.8 years ago by
pragathi.sneha91
• 0
0
votes
3
replies
3.4k
views
Help with Salmon --> tximport --> edgeR
RNA-Seq
tximport
salmon
edgeR
normalisation
updated 2.8 years ago by
lieven.sterck
15k • written 4.4 years ago by
u3005992
▴ 20
1
vote
1
reply
818
views
Tximport "sclaedTPMs" imports NumReads column from Salmon output
TPMs
salmon
tximport
rna-seq
updated 2.9 years ago by
jared.andrews07
★ 17k • written 2.9 years ago by
anna
• 0
4
votes
2
replies
971
views
Transcriptional noise detection and Salmon TPMs
salmon
isoforms
tximport
rna-seq
tpms
3.1 years ago by
karlaarz
▴ 110
0
votes
2
replies
2.0k
views
When importing my quant.sf files into R using tximport, should I set 'ignoreTxVersion' to True or False?
Salmon
RNA-Seq
tximport
R
updated 3.1 years ago by
jaro.slamecka
▴ 270 • written 3.1 years ago by
robeaumont
• 0
2
votes
10
replies
3.9k
views
6 follow
How do I match my transcript ID's from NCBI to the corresponding gene ID's to enable tximport into R?
Salmon
tximport
RNA-Seq
R
updated 2.2 years ago by
GenoMax
145k • written 3.1 years ago by
robeaumont
• 0
0
votes
2
replies
1.2k
views
tximport for gene level summarization of 9 quant.sf files
salmon
tximport
rna-seq
updated 3.4 years ago by
Ram
44k • written 3.4 years ago by
Cody
• 0
0
votes
4
replies
1.9k
views
Help with salmon quantification of samples with de novo transcriptome
salmon
denovo
tximport
updated 3.5 years ago by
ponganta
▴ 590 • written 3.5 years ago by
codyas
• 0
4
votes
10
replies
2.1k
views
Importing quant.sf file to tximport
software-error
tximport
genome
updated 15 months ago by
Ram
44k • written 3.5 years ago by
yvarg009
• 0
3
votes
2
replies
5.1k
views
Tximport > DESeq2 (sample names)
DESeq2
tximport
RNA-Seq
updated 3.9 years ago by
skgtjzw
• 0 • written 5.8 years ago by
Barry Digby
★ 1.3k
0
votes
4
replies
2.0k
views
Problem with gene names in tximport
tximport
RNA-Seq
rna-seq
R
updated 4.1 years ago by
Biostar
20 • written 4.3 years ago by
dioscorea.bulbifera
▴ 10
1
vote
5
replies
2.0k
views
How to fix extreme outliers not picked up by DESeq2?
DESeq2
RNA-Seq
Outlier
Cook's Distance
TXImport
updated 4.1 years ago by
antonioggsousa
3.2k • written 4.1 years ago by
fisher.w.daniel
• 0
1
vote
0
replies
874
views
Import Salmon output by tximport
RNA-Seq
R
tximport
salmon
updated 4.2 years ago by
Ram
44k • written 4.2 years ago by
koaeb
▴ 10
0
votes
2
replies
2.7k
views
RSEM isoform.results outputs for edgeR
rsem
tximport
edgeR
4.2 years ago by
weichengz
• 0
3
votes
3
replies
8.7k
views
Kallisto and downstream analysis with tximport and DESeq2
RNA-Seq
kallisto
tximport
deseq2
4.3 years ago by
Mozart
▴ 330
3
votes
4
replies
1.8k
views
Tximport Error ... unable to match up my quant.sf and tx2gene columns
RNA-Seq
Tximport
salmon
4.3 years ago by
2405592M
▴ 150
0
votes
3
replies
1.3k
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq
deseq2
tximport
salmon
4.3 years ago by
tianshenbio
▴ 180
2
votes
10
replies
3.7k
views
error in TXIMPORT command for RSEM
tximport
rsem
updated 4.4 years ago by
Kevin Blighe
88k • written 4.4 years ago by
StartR
▴ 30
1
vote
2
replies
922
views
error in tximport command
tximport
updated 4.4 years ago by
ATpoint
84k • written 4.4 years ago by
StartR
▴ 30
3
votes
1
reply
1.8k
views
tximport --> edgeR
tximport
edgeR
RNA-Seq
4.4 years ago by
u3005992
▴ 20
1
vote
5
replies
3.1k
views
How is the bootstrapping information from kallisto treated in DeSeq2 when imported using tximport?
RNA-Seq
kallisto
deseq2
tximport
updated 4.5 years ago by
ATpoint
84k • written 4.5 years ago by
divya.nandakumar
▴ 30
0
votes
1
reply
1.3k
views
Issue with Salmon and Deseq2 with paired-end and single-end reads libraries
salmon
deseq2
rnaseq
tximport
updated 7 months ago by
Natalie
• 0 • written 4.6 years ago by
Andrés Ribone
▴ 60
0
votes
2
replies
2.4k
views
DESeq2 Error: Error: $ operator is invalid for atomic vectors
RNA-Seq
DESeq2
deseq2
tximport
updated 4.9 years ago by
Biostar
20 • written 5.0 years ago by
Ulduz
▴ 20
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