Showing : Tximport • reset
16
votes
25
replies
3.7k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.7 years ago by ▴ 60
2
votes
19
replies
2.9k
views
tximport returns NA counts
tximport
7.1 years ago leonfodoulian • 0
2
votes
18
replies
3.8k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.7 years ago stephan.emmrich ▴ 10
7
votes
17
replies
6.0k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
7.6 years ago JWCarlson ▴ 80
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.6 years ago by ▴ 20 • written 8.4 years ago by ▴ 200
2
votes
14
replies
2.5k
views
Salmon (quant.sf) to tximport error
tximport
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
4
votes
14
replies
3.1k
views
running tximport for salmon quants
tximport readr
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
3
votes
13
replies
2.7k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
6.8 years ago tim.ivanov.92 • 0
4
votes
13
replies
2.6k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
8
votes
12
replies
4.3k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 7.2 years ago by ★ 2.1k • written 7.2 years ago by • 0
10
votes
11
replies
2.7k
views
tximport error: vroom
tximport
updated 13 months ago by • 0 • written 14 months ago by ▴ 40
1
vote
11
replies
7.7k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
7.2 years ago tanyabioinfo ▴ 20
2
votes
11
replies
2.3k
views
failure importing data with tximport with error information
software error tximport hdf5
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
6
votes
11
replies
2.5k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
5.6 years ago • updated 4.9 years ago ATpoint ★ 4.6k
3
votes
11
replies
2.9k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.8 years ago by ▴ 20 • written 8.7 years ago by ▴ 10
5
votes
10
replies
12k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
6
votes
10
replies
2.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 months ago by • 0 • written 22 months ago by ▴ 10
0
votes
10
replies
2.5k
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 5.4 years ago by 43k • written 5.4 years ago by • 0
5
votes
9
replies
3.9k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.9 years ago emmak ▴ 20
1
vote
9
replies
1.7k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 20
4
votes
9
replies
2.6k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ★ 2.0k
3
votes
9
replies
5.6k
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
5.8 years ago Leo K • 0
2
votes
9
replies
1.7k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
17 months ago Ndimensional ▴ 20
2
votes
9
replies
1.5k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
4
votes
9
replies
4.9k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 18 months ago by • 0 • written 7.5 years ago by • 0
5
votes
9
replies
5.9k
views
Trouble with Tximport
tximport salmon
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 30
1
vote
9
replies
3.4k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
vote
9
replies
2.9k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 5.7 years ago by ▴ 120 • written 5.7 years ago by • 0
2
votes
9
replies
2.3k
views
Unused argument of reader = read_tsv on R version 3.4.1
tximport
7.3 years ago tarun2 • 0
0
votes
8
replies
1.6k
views
tximport question on the values contained in "counts" and "abundance" matrices
tximport
updated 5.8 years ago by 67k • written 5.9 years ago by • 0
2
votes
8
replies
901
views
Silent error in tximport after installing GEOquery
tximport
5.3 years ago penny.lane • 0
7
votes
8
replies
4.4k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 5.9 years ago by 0 • written 6.1 years ago by ▴ 20
0
votes
8
replies
2.4k
views
tximport not working on tsv files
tximport
5.4 years ago • updated 5.3 years ago HKS • 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 • updated 2.4 years ago Kelen ▴ 10
0
votes
8
replies
2.3k
views
Importing RSEM with tximport
tximport RSEM import error
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 60
2
votes
8
replies
4.4k
views
Which R version is needed for tximport package?
tximport package R version install tximport
4.3 years ago harelarik ▴ 60
0
votes
8
replies
2.9k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
8
replies
3.3k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
5.2 years ago k1m ▴ 20
2
votes
7
replies
3.0k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
votes
7
replies
2.3k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
3
votes
7
replies
1.5k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
19 months ago Yijing • 0
2
votes
7
replies
2.4k
views
Obtaining transcript names in RSEM
tximport rsem
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
1
vote
7
replies
2.6k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 3.7 years ago by • 0 • written 4.6 years ago by ▴ 50
1
vote
7
replies
2.3k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2 tximport
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
4
votes
7
replies
4.7k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
0
votes
7
replies
2.0k
views
Problem with Tximport
tximportData tximport
3.9 years ago agoesmartini • 0
0
votes
7
replies
2.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 3.1 years ago by • 0 • written 7.6 years ago by ▴ 40
2
votes
7
replies
2.5k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 6.3 years ago by 52k • written 6.3 years ago by • 0
0
votes
7
replies
1.3k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
4.8 years ago rafaelsolersanblas ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Comment: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Comment: Help using rtracklayer for gene ID extraction by Aichatou • 0
Hello, Please disregard the previous post. it's working now, i think. I am able to create the txdb object but I can't see all the other inf…
Comment: p value is 0, padj is 0 by Wirayatida • 0
Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.
Comment: p value is 0, padj is 0 by Wirayatida • 0
Thank you so much for your information. I understand it.
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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