Showing : tximport • reset
1
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2
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380
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
6 days ago • updated 5 days ago georgii.vdovin • 0
4
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5
replies
612
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 weeks ago LuciaNhu • 0
0
votes
2
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371
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
0
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2
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415
views
tximport data import
tximport
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
2
replies
782
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
4 months ago grothmn • 0
1
vote
2
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2.2k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 6 months ago by ▴ 40 • written 5.1 years ago by • 0
0
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4
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598
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
6 months ago JG13 • 0
0
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2
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544
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
8 months ago Marianna ▴ 20
0
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2
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580
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 months ago by 43k • written 8 months ago by • 0
2
votes
1
reply
500
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
2
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3
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2.4k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
votes
1
reply
705
views
tximport error with rsem files
rsem tximport
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
3
votes
2
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975
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 12 months ago by 67k • written 12 months ago by • 0
0
votes
3
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802
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 14 months ago by 43k • written 14 months ago by • 0
10
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11
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2.8k
views
tximport error: vroom
tximport
updated 13 months ago by • 0 • written 14 months ago by ▴ 40
2
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3
replies
1.2k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 16 months ago by • 0
4
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13
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2.6k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
0
votes
4
replies
1.4k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 15 months ago by 43k • written 16 months ago by • 0
1
vote
2
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2.2k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 16 months ago by ▴ 120 • written 16 months ago by ▴ 10
2
votes
9
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1.7k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
17 months ago Ndimensional ▴ 20
0
votes
2
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924
views
tximport error in reading salmon output files?
tximport tximportData
updated 10 months ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
903
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 19 months ago by 67k • written 19 months ago by • 0
2
votes
1
reply
1.0k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 19 months ago by 43k • written 19 months ago by • 0
3
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7
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1.5k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
19 months ago Yijing • 0
0
votes
2
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1.2k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
20 months ago • updated 19 months ago Yijing • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
2
replies
1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
1
vote
5
replies
1.6k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 22 months ago by 43k • written 22 months ago by ▴ 90
6
votes
10
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2.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 8 months ago by • 0 • written 22 months ago by ▴ 10
0
votes
1
reply
963
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 23 months ago by ★ 1.5k • written 23 months ago by ▴ 10
0
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2
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1.2k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 23 months ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
2
votes
1
reply
989
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
2
votes
5
replies
1.9k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 months ago by 43k • written 24 months ago by • 0
0
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2
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1.1k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.0 years ago Konstantinos • 0
2
votes
3
replies
1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.0 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.1 years ago by ★ 4.6k • written 2.1 years ago by • 0
1
vote
2
replies
1.0k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.1 years ago cta • 0
2
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3
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1.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.2 years ago by ▴ 50
3
votes
3
replies
1.4k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.2 years ago • updated 2.1 years ago duhwa.lee • 0
1
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2
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2.0k
views
transcripts missing from tx2gene
tximport
2.2 years ago Erick • 0
0
votes
1
reply
883
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
2
votes
1
reply
2.6k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by ▴ 10
3
votes
4
replies
1.8k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
0
votes
3
replies
1.2k
views
tximport error
error tximport
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
5
votes
6
replies
1.9k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
0
votes
4
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1.5k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.5 years ago uhlkatie • 0
1
vote
3
replies
2.3k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.5 years ago Kelen ▴ 10
50 results • Page 1 of 1
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
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I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…
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Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
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