Showing : TXIMPORT • reset
0
votes
2
replies
167
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 2 days ago by 42k • written 2 days ago by • 0
0
votes
2
replies
342
views
tximport data import
tximport
updated 29 days ago by 42k • written 4 weeks ago by • 0
1
vote
2
replies
660
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
9 weeks ago • updated 8 weeks ago grothmn • 0
1
vote
2
replies
2.1k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 4 months ago by ▴ 40 • written 4.9 years ago by • 0
0
votes
4
replies
509
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
4 months ago JG13 • 0
0
votes
2
replies
441
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 months ago Marianna ▴ 20
0
votes
2
replies
446
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 6 months ago by 42k • written 6 months ago by • 0
2
votes
1
reply
430
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
2
votes
3
replies
2.0k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by • 0
0
votes
1
reply
591
views
tximport error with rsem files
rsem tximport
updated 9 months ago by ★ 4.5k • written 9 months ago by • 0
3
votes
2
replies
868
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 10 months ago by 67k • written 10 months ago by • 0
0
votes
3
replies
690
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 11 months ago by 42k • written 11 months ago by • 0
10
votes
11
replies
2.5k
views
tximport error: vroom
tximport
updated 11 months ago by • 0 • written 12 months ago by ▴ 40
2
votes
3
replies
1.1k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 13 months ago by • 0
4
votes
13
replies
2.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 12 months ago by 42k • written 13 months ago by • 0
0
votes
4
replies
1.3k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 13 months ago by 42k • written 13 months ago by • 0
1
vote
2
replies
2.1k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 14 months ago by ▴ 120 • written 14 months ago by ▴ 10
2
votes
9
replies
1.6k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
15 months ago Ndimensional ▴ 20
0
votes
2
replies
861
views
tximport error in reading salmon output files?
tximport tximportData
updated 8 months ago by • 0 • written 15 months ago by • 0
0
votes
1
reply
837
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 16 months ago by 67k • written 16 months ago by • 0
2
votes
1
reply
903
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 17 months ago by 42k • written 17 months ago by • 0
3
votes
7
replies
1.4k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
17 months ago Yijing • 0
0
votes
2
replies
1.1k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
17 months ago Yijing • 0
1
vote
3
replies
1.1k
views
tximport error
tximport r
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
2
replies
1.2k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 19 months ago by ★ 4.5k • written 19 months ago by • 0
1
vote
5
replies
1.5k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 19 months ago by 42k • written 19 months ago by ▴ 90
6
votes
10
replies
2.4k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 5 months ago by • 0 • written 20 months ago by ▴ 10
0
votes
1
reply
906
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 20 months ago by ★ 1.5k • written 20 months ago by ▴ 10
0
votes
2
replies
1.1k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 21 months ago by • 0
0
votes
1
reply
989
views
Missing transcript
DESeq2 tximport salmon
updated 21 months ago by ★ 4.5k • written 21 months ago by • 0
2
votes
1
reply
912
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 21 months ago by ★ 4.5k • written 21 months ago by • 0
2
votes
5
replies
1.7k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 7 months ago by 42k • written 21 months ago by • 0
0
votes
2
replies
999
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
22 months ago Konstantinos • 0
2
votes
3
replies
1.5k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
22 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.3k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 22 months ago by 67k • written 22 months ago by ▴ 10
0
votes
1
reply
1.1k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
1
vote
2
replies
977
views
error loading kallisto output in tximport
file.exists false kallisto tximport
23 months ago cta • 0
2
votes
3
replies
1.6k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 23 months ago by ▴ 50
3
votes
3
replies
1.2k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
23 months ago duhwa.lee • 0
1
vote
2
replies
1.9k
views
transcripts missing from tx2gene
tximport
2.0 years ago Erick • 0
0
votes
1
reply
821
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.0 years ago by 42k • written 2.0 years ago by • 0
2
votes
1
reply
2.2k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.1 years ago by ★ 4.5k • written 2.1 years ago by ▴ 10
3
votes
4
replies
1.7k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.1 years ago by ★ 4.5k • written 2.1 years ago by • 0
0
votes
3
replies
1.2k
views
tximport error
error tximport
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
5
votes
6
replies
1.8k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.1 years ago by 51k • written 2.1 years ago by • 0
0
votes
4
replies
1.4k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.3 years ago uhlkatie • 0
1
vote
3
replies
2.1k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
2
votes
8
replies
1.9k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.3 years ago Kelen ▴ 10
0
votes
1
reply
1.3k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.4 years ago by ★ 4.5k • written 2.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Hi Maria, so what is the code you are using? By the 3rd way to conduct the analysis do you mean looking at the interaction model from part …
Comment: miRTarRnaseq library by María Calvo • 0
Hello, in line with the previous questions, when the miRNA-mRNA interaction analysis is performed (3 rd way to conduct the analysis), I obt…
Answer: heatmap with batch effect by James W. MacDonald 67k
You have only one condition in the second batch, so it's not possible to remove the batch effect. You can probably adjust for it somewhat, …
Answer: how do I convert an Ilumn IDREF to a CPG loci by James W. MacDonald 67k
``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame with 865859 rows and 3 columns ch…
Answer: Which input data is acceptable for MAST? by Andrew_McDavid ▴ 270
Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…
Votes
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
Answer: How to control batch effect if Group and batch are same?
Awards • All
Popular Question to Andrew_McDavid ▴ 270
Scholar to Ryan C. Thompson ★ 7.9k
Popular Question to Basti ▴ 780
Popular Question to Gordon Smyth 51k
Popular Question to shepherl 4.0k
Locations • All
France, 2 minutes ago
United States, 39 minutes ago
United States, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
UPF, Barcelona, Spain, 3 hours ago
Traffic: 1048 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6