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QuasR
•
reset
0
votes
7
replies
3.5k
views
'CreateProcess' failed to run error with Rbowtie
software error
quasr
rbowtie
9.6 years ago
annabel.ferguson
• 0
0
votes
6
replies
3.3k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster
quasR
genomicfeatures
genomicranges
alignment
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
Fiona
▴ 70
0
votes
2
replies
1.5k
views
QuasR question
QuasR
updated 9.7 years ago by
Daniel Soronellas
▴ 10 • written 9.7 years ago by
Michael Stadler
▴ 350
0
votes
3
replies
1.1k
views
QuasR::qAlign: how to specify maximum allowed number of mismatches and output all alignments
QuasR
updated 4.4 years ago by
Michael Stadler
▴ 350 • written 4.4 years ago by
Julie Zhu
★ 4.3k
0
votes
8
replies
3.2k
views
QuasR: how to use an indexed reference genome?
BSgenome
BSgenome
genomes
QuasR
BSgenome
BSgenome
genomes
QuasR
updated 11.0 years ago by
Michael Stadler
▴ 350 • written 11.0 years ago by
Paul Shannon
▴ 750
0
votes
2
replies
1.8k
views
quasR - how are exon identifiers for exon counts determined
rnaseq
exon
quasr
updated 9.4 years ago by
Steve Lianoglou
★ 13k • written 9.4 years ago by
sven.schuierer
• 0
2
votes
5
replies
2.1k
views
QuasR: Loading BAM files as start point
quasr
updated 8.7 years ago by
Michael Stadler
▴ 350 • written 8.7 years ago by
rahel14350
▴ 10
0
votes
5
replies
1.8k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq
quasr
alignment
updated 8.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.4 years ago by
nadia_boufaied
• 0
2
votes
1
reply
851
views
preprocessReads: Can't remove more than 17 nucleotides
QuasR
preprocessReads
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
sha-ked
• 0
0
votes
7
replies
2.6k
views
QuasR on Linux Cluster
BSgenome
BSgenome
QuasR
BSgenome
BSgenome
QuasR
updated 10.5 years ago by
Michael Stadler
▴ 350 • written 10.6 years ago by
Ugo Borello
▴ 340
1
vote
1
reply
2.0k
views
multiple threads on QuasR
Alignment
GLAD
QuasR
Alignment
GLAD
QuasR
11.1 years ago • updated 11.0 years ago
Michael Stadler
▴ 350
0
votes
2
replies
1.2k
views
QuasR special case alignment
Alignment
QuasR
Alignment
QuasR
updated 11.0 years ago by
Michael Stadler
▴ 350 • written 11.0 years ago by
Ugo Borello
▴ 340
0
votes
2
replies
1.6k
views
QuasR special case alignment
Alignment
genomes
QuasR
Alignment
genomes
QuasR
updated 11.0 years ago by
Ugo Borello
▴ 340 • written 11.0 years ago by
Michael Stadler
▴ 350
0
votes
3
replies
1.6k
views
Summarization by gene or exon or transcript
QuasR
QuasR
10.5 years ago
Michael Stadler
▴ 350
0
votes
7
replies
2.1k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment
Rattus norvegicus
BSgenome
BSgenome
QuasR
Alignment
Rattus norvegicus
BSgenome
updated 10.2 years ago by
Hervé Pagès
16k • written 10.2 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
1.1k
views
QuasR - importing alignment files from other aligners
quasr
updated 9.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 9.4 years ago by
sven.schuierer
• 0
0
votes
2
replies
1.3k
views
QuasR alignment interruption
quasr
updated 8.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.3 years ago by
nadia_boufaied
• 0
0
votes
1
reply
1.3k
views
Postdoctoral research fellow
QuasR
updated 8.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.3 years ago by
tarek.mohamed
▴ 10
0
votes
1
reply
1.4k
views
QuasR: spliced and unspliced alignment
quasr
alignment
updated 8.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.3 years ago by
nadia_boufaied
• 0
2
votes
4
replies
1.6k
views
Bowtie % mapped reads for DGE
Bowtie
quasr
rnaseq
updated 8.3 years ago by
Dario Strbenac
★ 1.5k • written 8.3 years ago by
tarek.mohamed
▴ 10
0
votes
3
replies
1.5k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap
QuasR
RNAseq
Alignment
updated 8.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.3 years ago by
tarek.mohamed
▴ 10
0
votes
4
replies
1.7k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR
rnaseq
alignment
splicemap
bowtie2
8.2 years ago • updated 8.1 years ago
Gabriella
• 0
1
vote
1
reply
3.3k
views
ERROR: lazy loading failed for package 'QuasR'
QuasR
updated 8.1 years ago by
Martin Morgan
25k • written 8.1 years ago by
Hackerzone85
• 0
1
vote
6
replies
1.6k
views
Multithreading problems with qalign
quasr
parallel
updated 7.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 7.4 years ago by
kirt.onthank
• 0
1
vote
1
reply
1.0k
views
QuasR error message
QuasR
RNA_Seq
updated 6.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 6.4 years ago by
ta_awwad
▴ 10
1
vote
4
replies
1.1k
views
qQCReport Missing Plots Described in Documentation
QuasR
updated 5.2 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 5.2 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
770
views
using qCount from the QuasR package
qCount
QuasR
NA
updated 3.8 years ago by
Michael Stadler
▴ 350 • written 3.8 years ago by
jabbar_campbell
• 0
0
votes
1
reply
787
views
RNAseq analysis of organism not included in BSgenome using QuasR
QuasR
updated 3.6 years ago by
Michael Stadler
▴ 350 • written 3.6 years ago by
anuranjansrathore
• 0
0
votes
1
reply
1.0k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl
Alignment
QuasR
updated 3.2 years ago by
Michael Stadler
▴ 350 • written 3.2 years ago by
h.kozlowski
• 0
0
votes
0
replies
947
views
Error preprocessReads : Error in writeFastq
quasr
rnaseq
paired-end reads
7.4 years ago
guillaume.dachy
• 0
0
votes
1
reply
1.1k
views
Memory error building index
QuasR
updated 9.6 years ago by
Martin Morgan
25k • written 9.6 years ago by
hmabril
• 0
0
votes
0
replies
1.2k
views
QuasR for miRNA
miRNA
QuasR
miRNA
QuasR
10.0 years ago
Michael Stadler
▴ 350
0
votes
0
replies
1.1k
views
Error in qAlign, QuasR, in paired-end RNA Seq
quasr
paired-end reads
rnaseq
7.3 years ago
guillaume.dachy
• 0
0
votes
0
replies
939
views
RNA Seq // QuasR : Error while extracting unmapped reads
quasr
quasr error
paired-end reads
rnaseq
7.3 years ago
guillaume.dachy
• 0
1
vote
0
replies
1.6k
views
QuasR - preprocessReads fails with a SRFilterResult error
quasr
quasr error
7.2 years ago
jlncrnt
▴ 10
0
votes
0
replies
871
views
can not depends QuasR in another package
QuasR
6.9 years ago
zwfanwz678
• 0
0
votes
1
reply
1.1k
views
qCount with a GRangesList is very slow
QuasR
qCount
GRangesList
6.8 years ago
vakul.mohanty
▴ 20
0
votes
9
replies
2.2k
views
problem using >3 clusters with Quasr
quasr
parallel
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
rna seq
▴ 90
0
votes
1
reply
1.2k
views
error when genomeFile too big when running Quasr on >3 clusters
quasr
parallel
cluster
8.2 years ago
rna seq
▴ 90
0
votes
0
replies
1.8k
views
Create a sample file /tab delimited file in QuasR
BSgenome
convert
BSgenome
genomes
QuasR
BSgenome
convert
BSgenome
genomes
QuasR
10.5 years ago
Michael Stadler
▴ 350
1
vote
2
replies
1.3k
views
Error in checkForRemoteErrors(val) : QuasR: can't pass alignment parameters
quasR
quasr error
alignmentparameters
quasr
5.5 years ago
Amer Ghalawinji
• 0
0
votes
2
replies
1.3k
views
Fusion gene mutation detection
bioconductor
quasr
7.8 years ago
maedakus
▴ 10
0
votes
0
replies
1.4k
views
Create a sample file /tab delimited file in QuasR
BSgenome
convert
BSgenome
QuasR
BSgenome
convert
BSgenome
QuasR
10.5 years ago
Guest User
★ 13k
43 results • Page
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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