Showing : txImport • reset
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472
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tximport in DESeq2 problem
tximport
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
2
votes
3
replies
2.8k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
6.3 years ago Benjamin • 0
1
vote
2
replies
1.1k
views
Data downloaded from GEO has raw transcript count matrix- can I still use tximport? Collapse raw transcript count matrix to GENE LEVEL
tximport collapse
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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1
reply
756
views
Get gene level summaries from table of transcript level quantification
tximport deseq2
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
1
vote
4
replies
1.7k
views
tximport from Galaxy output
normalization tximport
updated 3.9 years ago by • 0 • written 6.3 years ago by ▴ 20
1
vote
2
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1.4k
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 50
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6
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1.5k
views
tximport discrepancy between TPMs and lengthScaledTPMs
tximport
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 50
1
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1
reply
1.3k
views
inferential replicates in Kallisto when summarising values via tximport
tximport
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
2
votes
6
replies
1.3k
views
Importing transcript abundance datasets generated with Salmon 0.14.0
tximport
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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6
replies
2.0k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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3
replies
868
views
Salmon / tximport
tximport deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
4
votes
1
reply
1.5k
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
3
votes
1
reply
2.4k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
0
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1
reply
1.1k
views
Robust FPM with normalization factors (from tximport)?
deseq2 tximport normalization
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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3
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1.0k
views
output of the function "makeCountsFromAbundance"
tximport
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
1
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2
replies
1.3k
views
tximport and txOut
tximport deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Tximport error (probably annotation lowercase incompatibility)
arabidopsis tximport gtf annotation
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
9
replies
3.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 6.6 years ago by ▴ 120 • written 6.6 years ago by • 0
16
votes
25
replies
4.5k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 6.6 years ago by ▴ 60
3
votes
4
replies
2.4k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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4
replies
3.3k
views
Error in H5Fopen with kallisto .h5 files
tximport kallisto rhdf5
6.6 years ago uso2015 • 0
2
votes
14
replies
3.1k
views
Salmon (quant.sf) to tximport error
tximport
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
2
votes
6
replies
2.6k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
3
replies
2.6k
views
Counts, abundance in Tximport
Tximport
6.6 years ago hong • 0
3
votes
9
replies
6.3k
views
txi <- tximport(files, type="salmon", tx2gene=tx2gene) Error in tximport(files, type = "salmon", tx2gene = tx2gene) : all(file.exists(files)) is n…
deseq2 tximport file.path files file.exists
6.7 years ago • updated 6.6 years ago Leo K • 0
0
votes
6
replies
2.5k
views
[deseq2] normalization between samples after merging transcripts into genes
deseq2 tximport
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
8
replies
2.0k
views
tximport question on the values contained in "counts" and "abundance" matrices
tximport
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
votes
4
replies
2.5k
views
Htseq files import via tximport
tximport importer
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
votes
1
reply
1.1k
views
tximport: question concerning 'bias corrected counts without an offset' method
tximport deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
vote
1
reply
1.3k
views
DESeqFromMatrix for 3'end data via tximport; non-integer values
deseq2 tximport
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 20
0
votes
4
replies
2.4k
views
tximport: Error in medianLengthOverIsoform
tximport deseq2 dexseq
6.7 years ago d-joester ▴ 20
1
vote
4
replies
2.5k
views
Error : Salmon tximport to DESeq2
deseq2 tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
vote
5
replies
3.7k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
7
votes
8
replies
5.1k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 6.8 years ago by 0 • written 6.9 years ago by ▴ 20
2
votes
3
replies
2.1k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport kallisto
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 40
1
vote
1
reply
1.4k
views
tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DESeq2
tximport deseq2 rnaseq 3' tagged RNA
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 50
5
votes
2
replies
2.1k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
votes
4
replies
1.8k
views
tximport and its version
tximport stringtie RNA-seq analysis
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
votes
2
replies
1.1k
views
Getting an error trying to do tximportData tutorial
deseq2 tximport
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
1
vote
4
replies
1.1k
views
importing Tximport to DESeq2 for a time series experiment
deseq2 tximport
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
1
reply
830
views
How tximport summerize transcript-level abundance to gene-level
tximport
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
1
reply
3.2k
views
How get genename by tximport
tximport genename
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
vote
2
replies
1.4k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
7.0 years ago fcuy047 • 0
1
vote
2
replies
1.6k
views
trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
3
votes
4
replies
2.1k
views
tximport and de novo transcriptome
tximport salmon rna seq de novo
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 10
1
vote
4
replies
1.1k
views
Help with error produced when using makeTxDbFromBiomart
tximport tximport rnaseq
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
2
votes
7
replies
3.0k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
1
vote
2
replies
2.9k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport ensembldb bos taurus tx2gene
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
1
reply
1.6k
views
DESeq2/tximport 'duplicate rownames not allowed' error
tximport deseq2
7.2 years ago ctl • 0
297 results • Page 4 of 6
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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