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rsubread
•
reset
12
votes
7
replies
3.3k
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql
shortread
Rsubread
updated 6.4 years ago by
Aspie96
▴ 60 • written 6.4 years ago by
Raito92
▴ 60
2
votes
6
replies
2.7k
views
featurecounts Rsubread ERROR on exon_id
R
error
software error
Rsubread
featurecounts
updated 6.4 years ago by
Wei Shi
★ 3.6k • written 6.4 years ago by
edejong
• 0
1
vote
2
replies
2.1k
views
Problem with importing text file in featureCounts
Rsubread
featureCounts
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
estevemp
• 0
3
votes
4
replies
1.3k
views
Featurecount -- normalized Path error
path
Rsubread
updated 6.5 years ago by
cellfixnowusa
• 0 • written 6.6 years ago by
memoly101
• 0
3
votes
13
replies
3.9k
views
Rsubread- feature counts
annotation
Rsubread
featureCounts
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
memoly101
• 0
0
votes
2
replies
1.8k
views
Data import with read.delim
limma
rsubread
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
justinkablan225
▴ 10
0
votes
9
replies
3.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
6.8 years ago
A
▴ 60
0
votes
9
replies
4.0k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts
Rsubread
ggbio
updated 6.8 years ago by
Wei Shi
★ 3.6k • written 6.8 years ago by
A
▴ 60
2
votes
1
reply
1.5k
views
Rsubread for microbiome data analysis: genome >4GB
alignment
rsubread
microbiome
updated 6.8 years ago by
Wei Shi
★ 3.6k • written 6.8 years ago by
W. Evan Johnson
▴ 870
0
votes
16
replies
5.4k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
6.9 years ago
writetoroopali
• 0
4
votes
7
replies
7.7k
views
convert featureCounts's gene ID to entrez gene id
biomart
rsubread
gencode
updated 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
YinCY
▴ 20
1
vote
2
replies
1.3k
views
I am unable to use Rsubread. Thank you in advance.
rsubread
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
Mithil Gaikwad
• 0
3
votes
4
replies
1.8k
views
File not found error when using dupRadar::analyzeDuprates
dupradar
rsubread
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
b.nota
▴ 370
0
votes
4
replies
1.4k
views
Is circular RNA read out as linear fragments during Rsubread-DESeq2
deseq2
circrna
rsubread
updated 7.2 years ago by
Wei Shi
★ 3.6k • written 7.2 years ago by
csijst
• 0
0
votes
8
replies
4.5k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread
featurecounts
7.2 years ago
connor.geraghty
• 0
9
votes
16
replies
3.7k
views
Rsubread install fails, "unable to load shared object Rsubread.so"
rsubread
7.3 years ago
jet456
▴ 10
1
vote
6
replies
2.5k
views
Rsubread Installation error
rsubread
compilation error
updated 7.4 years ago by
Gordon Smyth
52k • written 7.4 years ago by
chitsazanalex
▴ 10
1
vote
4
replies
2.0k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq
rsubread
featurecounts
updated 7.5 years ago by
Wei Shi
★ 3.6k • written 7.5 years ago by
mmurshed
• 0
0
votes
1
reply
1.3k
views
how to create index
Rsubread
updated 7.6 years ago by
Mike Smith
★ 6.6k • written 7.6 years ago by
Bioinformatics
▴ 30
0
votes
1
reply
1.6k
views
Rsubread Read Bam and filter reads by TAG field
Rsubread
featurecounts
featurerequest
7.6 years ago
alessandro.pastore
▴ 20
0
votes
7
replies
2.9k
views
caught segfault when using featureCounts
rsubread
featurecounts
7.7 years ago
Ge Tan
▴ 20
5
votes
3
replies
6.7k
views
Rsubread counting peaks ATACseq
Rsubread
atac-seq
narrowpeaks
featurecounts
updated 7.8 years ago by
Wei Shi
★ 3.6k • written 7.8 years ago by
j.bergenstrahle
▴ 90
0
votes
6
replies
2.5k
views
Rsubread featureCounts with byReadGroup
rsubread
featurecounts
updated 7.9 years ago by
Yang Liao
▴ 450 • written 7.9 years ago by
Ge Tan
▴ 20
6
votes
5
replies
3.4k
views
reads alignment statistics
rsubread
bioconductor
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
C T
▴ 140
3
votes
4
replies
3.3k
views
nthreads option does NOT work in rsubread featureCounts
rsubread
updated 8.0 years ago by
Gordon Smyth
52k • written 8.0 years ago by
shao
▴ 100
1
vote
5
replies
4.0k
views
using paired end and single end data in featurecounts
featurecounts
rsubread
updated 8.1 years ago by
James W. MacDonald
68k • written 8.1 years ago by
nikelle.petrillo
• 0
1
vote
4
replies
2.5k
views
Rsubread install problems on CentOS 6.8/R3.4.1/gcc/4.8.2
linux
rsubread
installation
updated 8.1 years ago by
Mike Smith
★ 6.6k • written 8.1 years ago by
hjmangalam
• 0
0
votes
3
replies
3.3k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread
featurecounts
exon
mRNAseq
updated 8.2 years ago by
Wei Shi
★ 3.6k • written 8.2 years ago by
inah
▴ 10
0
votes
1
reply
2.0k
views
Using Rsubread with FASTA sequence files over 4 GB
Rsubread
buildindex
fastafile
updated 8.3 years ago by
Wei Shi
★ 3.6k • written 8.3 years ago by
bryan.penning
• 0
0
votes
2
replies
4.6k
views
Problem running featurecounts in Rsubread on GFF file
rsubread
featurecounts
gff
Grch38.p7 vs hg38
8.3 years ago
raf4
▴ 30
0
votes
5
replies
2.0k
views
Rsubread crash on Mac during alignment
software error
rsubread
8.6 years ago • updated 8.3 years ago
raf4
▴ 30
0
votes
1
reply
1.5k
views
% of assigned reads using Rsubread featureCounts useMetaFeatures
featurecounts
rsubread
8.5 years ago
IV
▴ 30
4
votes
1
reply
5.3k
views
Rsubread featureCounts with strand information
Rsubread
bam
rnaseq
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
rubi
▴ 110
0
votes
1
reply
1.1k
views
RSubread buildindex error
rsubread
updated 8.8 years ago by
Gordon Smyth
52k • written 8.8 years ago by
sh24
• 0
2
votes
2
replies
3.6k
views
featureCounts Parameters for Exon Junctions
rsubread
featureCounts
updated 8.8 years ago by
Wei Shi
★ 3.6k • written 8.8 years ago by
Dario Strbenac
★ 1.6k
0
votes
4
replies
2.7k
views
Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
rsubread
ncbi
GRCh38
hg38
updated 8.8 years ago by
Wei Shi
★ 3.6k • written 8.9 years ago by
jan.soderman
• 0
0
votes
16
replies
3.4k
views
Variance between runs of Rsubread
rsubread
alignment
reproducibility
8.9 years ago
Isaac Virshup
• 0
5
votes
6
replies
7.3k
views
How featureCounts define the gene length
featurecounts
rnaseq
rsubread
updated 3.7 years ago by
Gordon Smyth
52k • written 8.9 years ago by
Yiwei Niu
▴ 20
1
vote
2
replies
2.2k
views
Rsubread align for miRNAseq?
rsubread
miRNA
updated 8.9 years ago by
Wei Shi
★ 3.6k • written 8.9 years ago by
Ina Hoeschele
▴ 620
0
votes
3
replies
2.1k
views
Installing problem Bioconductor
Rsubread
updated 8.9 years ago by
Martin Morgan
25k • written 8.9 years ago by
tran_tim
▴ 10
1
vote
11
replies
3.4k
views
rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
rsubread
BWA
NGS
updated 9.0 years ago by
Wei Shi
★ 3.6k • written 9.0 years ago by
tarek.mohamed
▴ 10
0
votes
1
reply
1.6k
views
rsubread exactsnp ERROR "memory not mapped"
rsubread
exactSNP
updated 9.0 years ago by
Wei Shi
★ 3.6k • written 9.0 years ago by
tarek.mohamed
▴ 10
1
vote
21
replies
4.6k
views
Rsubread stopping half-way through align
rsubread
9.2 years ago • updated 9.0 years ago
Campbell.1933
• 0
0
votes
10
replies
3.2k
views
Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
Rsubread
updated 9.0 years ago by
Wei Shi
★ 3.6k • written 9.2 years ago by
MWSchmid
• 0
3
votes
4
replies
2.0k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 9.1 years ago by
Gordon Smyth
52k • written 9.1 years ago by
thomas.dobrenel
• 0
2
votes
2
replies
2.1k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 17 months ago by
isaac.vock
• 0 • written 9.2 years ago by
Jon Manning
▴ 90
3
votes
5
replies
2.1k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts
rsubread
9.2 years ago
Hadi Gharibi
• 0
1
vote
5
replies
2.3k
views
Error using Rsubread align: caugh segfault invalid permissions
rsubread
align
segfault
updated 9.3 years ago by
Wei Shi
★ 3.6k • written 9.3 years ago by
gerard_llimos
▴ 10
5
votes
1
reply
3.8k
views
Tutorial:
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread
rsubread
ensembldb
Tutorial
9.4 years ago
phil.chapman
▴ 150
0
votes
2
replies
1.4k
views
negative value for minOverlap parameter
Rsubread
minOverlap
featureCounts
updated 9.4 years ago by
Wei Shi
★ 3.6k • written 9.4 years ago by
c.merce
• 0
208 results • Page
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Comment: voomLmFit fitted log-CPM values
by
Gordon Smyth
52k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values
by
Lina
▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values
by
Gordon Smyth
52k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Comment: EuroBioC2024 abstract submission is open!
by
Finnianfly
• 0
What specific requirements should be noted when preparing abstracts for presentation formats such as short talks, package demos, or posters…
Comment: Length of 'dimnames' [1] not equal to array extent
by
Francesco Silvestro
• 0
Resolved the error message!
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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