Showing : tximport • reset
1
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2
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401
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 days ago • updated 8 days ago georgii.vdovin • 0
4
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5
replies
615
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 weeks ago LuciaNhu • 0
0
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2
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372
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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 11 weeks ago by 43k • written 11 weeks ago by • 0
0
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2
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422
views
tximport data import
tximport
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
2
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791
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
4 months ago grothmn • 0
1
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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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601
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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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548
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
8 months ago Marianna ▴ 20
0
votes
2
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581
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 months ago by 43k • written 9 months ago by • 0
2
votes
1
reply
505
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
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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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982
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
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3
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811
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
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tximport error: vroom
tximport
updated 14 months ago by • 0 • written 14 months ago by ▴ 40
2
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3
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1.2k
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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 15 months ago by 43k • written 16 months ago by • 0
0
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4
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1.5k
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 17 months ago by ▴ 10
2
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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
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2
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927
views
tximport error in reading salmon output files?
tximport tximportData
updated 10 months ago by • 0 • written 18 months ago by • 0
0
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1
reply
908
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
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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
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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
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3
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1.3k
views
tximport error
tximport r
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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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
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5
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1.6k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 22 months ago by 43k • written 22 months ago by ▴ 90
6
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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
965
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
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1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
2
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1
reply
991
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Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
2
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5
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2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 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
2.1 years ago Konstantinos • 0
2
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3
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1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.1 years ago mohammedtoufiq91 ▴ 10
4
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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
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2
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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
886
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.3 years ago by 43k • written 2.3 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
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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
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3
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1.2k
views
tximport error
error tximport
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
5
votes
6
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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
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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
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3
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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
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8
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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
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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