Showing : tximport • reset
0
votes
1
reply
115
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 20 days ago by 63k • written 20 days ago by • 0
2
votes
1
reply
127
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 26 days ago by 40k • written 26 days ago by • 0
3
votes
7
replies
316
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
4 weeks ago • updated 28 days ago Yijing • 0
0
votes
2
replies
157
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
5 weeks ago Yijing • 0
1
vote
3
replies
188
views
tximport error
tximport r
updated 6 weeks ago by 40k • written 6 weeks ago by • 0
0
votes
2
replies
219
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 3 months ago by ★ 2.9k • written 3 months ago by • 0
1
vote
5
replies
355
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 3 months ago by 40k • written 3 months ago by ▴ 90
3
votes
5
replies
465
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
3 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
241
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 4 months ago by ★ 1.5k • written 4 months ago by • 0
0
votes
2
replies
318
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 4 months ago by • 0
0
votes
1
reply
235
views
Missing transcript
DESeq2 tximport salmon
updated 5 months ago by ★ 2.9k • written 5 months ago by • 0
2
votes
1
reply
243
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 5 months ago by ★ 2.9k • written 5 months ago by • 0
2
votes
2
replies
352
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
written 5 months ago by • 0
0
votes
2
replies
295
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
6 months ago Konstantinos • 0
2
votes
3
replies
523
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
6 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
421
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 6 months ago by 63k • written 6 months ago by ▴ 10
0
votes
1
reply
385
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 6 months ago by ★ 2.9k • written 6 months ago by • 0
1
vote
2
replies
336
views
error loading kallisto output in tximport
file.exists false kallisto tximport
6 months ago cta • 0
2
votes
2
replies
531
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
7 months ago L ▴ 50
3
votes
3
replies
362
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
7 months ago duhwa.lee • 0
1
vote
2
replies
583
views
transcripts missing from tx2gene
tximport
8 months ago Erick • 0
0
votes
1
reply
276
views
tximport: not all(file.exists(files)) are true
tximport
updated 8 months ago by 40k • written 8 months ago by • 0
2
votes
1
reply
578
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 8 months ago by ★ 2.9k • written 8 months ago by ▴ 10
3
votes
4
replies
451
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 8 months ago by ★ 2.9k • written 8 months ago by • 0
0
votes
3
replies
442
views
tximport error
error tximport
updated 8 months ago by 40k • written 9 months ago by • 0
5
votes
6
replies
683
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 8 months ago by 47k • written 9 months ago by • 0
0
votes
4
replies
521
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
11 months ago uhlkatie • 0
1
vote
3
replies
883
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 11 months ago by 40k • written 11 months ago by • 0
2
votes
8
replies
846
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
11 months ago Kelen ▴ 10
0
votes
1
reply
477
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 12 months ago by ★ 2.9k • written 12 months ago by ▴ 10
0
votes
1
reply
433
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 12 months ago by 40k • written 13 months ago by • 0
2
votes
3
replies
614
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
13 months ago Maka • 0
5
votes
4
replies
1.1k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
14 months ago Al90 ▴ 10
0
votes
2
replies
1.5k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
15 months ago nakane_clan • 0
2
votes
5
replies
1.1k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
15 months ago Marianna • 0
2
votes
3
replies
550
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 15 months ago by 40k • written 16 months ago by • 0
0
votes
1
reply
445
views
tximport
salmon tximport
updated 16 months ago by 40k • written 16 months ago by • 0
0
votes
1
reply
497
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 17 months ago by ★ 2.9k • written 17 months ago by • 0
0
votes
3
replies
875
views
tximport question on what counts to use for LogFC calculations
tximport
updated 18 months ago by 40k • written 18 months ago by • 0
0
votes
4
replies
987
views
Filtering output from tximport
tximport Salmon
updated 18 months ago by 40k • written 18 months ago by • 0
0
votes
1
reply
822
views
tximport samples with separate tx2gene maps
tximport
updated 19 months ago by 40k • written 20 months ago by • 0
1
vote
3
replies
1.7k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
19 months ago nicolette.sipperly • 0
2
votes
1
reply
938
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 20 months ago by 40k • written 20 months ago by • 0
0
votes
2
replies
890
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 21 months ago by 40k • written 21 months ago by • 0
1
vote
2
replies
770
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
22 months ago paulimer • 0
2
votes
3
replies
751
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 23 months ago by 63k • written 23 months ago by ▴ 40
2
votes
2
replies
726
views
Issues with Tximport
tximport
23 months ago bryce.thomas • 0
0
votes
4
replies
1.3k
views
Tximport error message - colnames
tximport
written 24 months ago by • 0
0
votes
5
replies
1.0k
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 24 months ago by 40k • written 2.0 years ago by • 0
4
votes
3
replies
898
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 2.0 years ago by 40k • written 2.0 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Bruno • 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output by betterwound • 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable by swbarnes2 ★ 1.2k
Did you relevel before or after calling DESeq?
Votes
Comment: Ensembl plants at annotationHub?
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
Answer: Although I successfully installed the package "simpleaffy'' , I cannot library i
Awards • All
Popular Question to Johannes Rainer ★ 2.0k
Popular Question to Jenn ▴ 30
Voter to swbarnes2 ★ 1.2k
Teacher to James W. MacDonald 63k
Popular Question to kyliecode • 0
Locations • All
University of Bologna, Bologna, Italy, 3 minutes ago
UPF, Barcelona, Spain, 8 minutes ago
Denmark, 12 minutes ago
Wageningen University, Wageningen, the Netherlands, 16 minutes ago
France, 29 minutes ago
Traffic: 516 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