Showing : txImport • reset
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944
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Error in importing Salmon quantifications into R with tximport
deseq2 tximport
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
1
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2
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1.1k
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How tximport calculate abundance
tximport abundance
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
2
votes
1
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2.0k
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tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 20
0
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4
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1.7k
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mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 620
6
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3
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4.0k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 40
1
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1
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1.6k
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Specifying tx2gene with tximeta
tximeta tximport
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
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2
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1.3k
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RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
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2
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3.0k
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tximport counts versus TPM
tximport TPM
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 620
2
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2
replies
3.4k
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DESeqDataSetFromTximport with and without offset
deseq2 tximport
5.3 years ago igor ▴ 50
6
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2
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1.5k
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tximport + edgeR not recommended?
tximport edgeR
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
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2
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1.6k
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Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
5.3 years ago keremwai • 0
4
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6
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3.0k
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Using spike-in RNA for normalization of Salmon counts imported using Tximport
deseq2 Tximport Sizefactors normalizationfactors spike-in
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
6
replies
3.3k
views
How to run tximport ?
tximport
updated 5.3 years ago by ★ 5.0k • written 5.3 years ago by • 0
1
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1
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597
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Unable to run tximport using sample.info ?
tximport deseq2 edgeR
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
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4
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1.8k
views
tximport importer isoform abundance
tximport
updated 2.4 years ago by ▴ 200 • written 5.3 years ago by ▴ 620
0
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3
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1.2k
views
tximport cannot inport RSEM FPKM data
tximport
updated 4.0 years ago by 43k • written 5.3 years ago by • 0
1
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1
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1.2k
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport DEXSeq-DTU DRIMSeq
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
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3
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1.3k
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RSEM and Tximport
RSEM tximport deseq2
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
2
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3
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1.4k
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Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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3
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2.0k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
6
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7
replies
3.8k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 9 months ago by 53k • written 5.4 years ago by ▴ 20
4
votes
7
replies
5.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
1
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7
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3.0k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 4.6 years ago by • 0 • written 5.4 years ago by ▴ 60
5
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5
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3.9k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
updated 4 months ago by 43k • written 5.5 years ago by • 0
1
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9
replies
4.0k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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4
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1.8k
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon tximport tximportdata ensembl
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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2
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1.2k
views
Parsing error creating tx2gene object for tximport
tximport GCF feature table parsing error chromosome
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
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0
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926
views
News: Importing alevin inferential replicates into R with tximport
tximport News
5.6 years ago Michael Love 43k
2
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4
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6.4k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
6.5 years ago • updated 5.6 years ago Mozart ▴ 30
0
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6
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1.6k
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tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 5.6 years ago by • 0 • written 5.6 years ago by • 0
0
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7
replies
1.7k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.7 years ago rafaelsolersanblas ▴ 50
0
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3
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3.3k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
reply
1.6k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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5
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2.8k
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Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport Gene IDs txdb RefSeq Salmon
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
6
votes
11
replies
3.1k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
6.4 years ago • updated 5.8 years ago ATpoint ★ 5.0k
1
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1
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1.3k
views
tximport errors with h5 and tsv files
tximport kallisto
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
3
votes
1
reply
833
views
Can tximport be used to mitigate sample specific length biases?
RNASeq tximport
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 30
2
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11
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2.8k
views
failure importing data with tximport with error information
software error tximport hdf5
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
5
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6
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4.9k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta ensembldb single-cell snRNA-seq tximport
updated 6.0 years ago by ★ 3.4k • written 6.0 years ago by ▴ 80
2
votes
4
replies
1.1k
views
Combining RSEM Files with dif row # for tximport
tximport DEseq2 RNAseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
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8
replies
3.9k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
6.1 years ago k1m ▴ 20
1
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2
replies
1.5k
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
2
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8
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1.2k
views
Silent error in tximport after installing GEOquery
tximport
6.1 years ago penny.lane • 0
2
votes
7
replies
2.9k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
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4
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1.5k
views
tximport query for un-normalized and TPM data
tximport
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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8
replies
2.8k
views
tximport not working on tsv files
tximport
6.2 years ago HKS • 0
0
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10
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3.3k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error RNAseq tximport R
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
3
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1.8k
views
windows tximport fail
tximport rhdf5
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
vote
7
replies
2.7k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2 tximport
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
5
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5
replies
6.1k
views
tximport transcript missing
deseq2 salmon tximport
6.3 years ago mr6518849 ▴ 10
297 results • Page 3 of 6
Recent ...
Replies
Comment: Interpretation of output of AffyRNAdeg and hist commands by debasainalsa • 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
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…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
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