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questions
0
votes
0
replies
387
views
Passing parameters to gyppy_duplex pipeline
base-calling
ont
oxford-nanopore
guppy
updated 9 months ago by
Ram
43k • written 9 months ago by
Parham
★ 1.6k
1
vote
1
reply
1.7k
views
Problem with loading data into Piano
piano
R
updated 17 months ago by
Ram
43k • written 8.8 years ago by
Parham
★ 1.6k
3
votes
6
replies
1.0k
views
Find strandness of sequences from raw sequences
strand
updated 2.4 years ago by
ATpoint
82k • written 2.4 years ago by
Parham
★ 1.6k
4
votes
10
replies
4.5k
views
How to find sequence patterns in genome?
pattern
genome
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Parham
★ 1.6k
0
votes
3
replies
1.2k
views
RnBeads iterates with an error "Warning in cor(x[i[i <= N]], y) : the standard deviation is zero"
rnbeads
methylation
updated 2.4 years ago by
mscherer
▴ 50 • written 2.5 years ago by
Parham
★ 1.6k
3
votes
3
replies
928
views
Methylation coordinates for hg19
methylation
cpg
updated 2.5 years ago by
lily
▴ 80 • written 2.5 years ago by
Parham
★ 1.6k
0
votes
0
replies
477
views
Mapping digested synthetic oligos back to original sequences.
shortread
digestion
map
2.7 years ago by
Parham
★ 1.6k
2
votes
1
reply
562
views
Package/script for random DNA generation with a pattern!
DNA
regex
methylation
updated 2.9 years ago by
Dunois
★ 2.5k • written 2.9 years ago by
Parham
★ 1.6k
0
votes
3
replies
3.0k
views
No GO-term and no ontology in goseq() output! What am I doing wrong?
goseq
GO-term
ontology
test.cats
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
1
vote
2
replies
692
views
How to create alternate reference for SNPs?
snps
reference
3.5 years ago by
Parham
★ 1.6k
0
votes
1
reply
1.8k
views
AnnotationHub Error in value[[3L]](cond) : failed to create index
annotationHUB
cache
annotation
updated 3.8 years ago by
Kevin Blighe
87k • written 3.8 years ago by
Parham
★ 1.6k
0
votes
2
replies
3.0k
views
How to create "design" for RNA-seq experiment using limma?
RNA-Seq
design
limma
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Parham
★ 1.6k
0
votes
0
replies
804
views
Split phased haplotypes of same person coming from same parents
variant
haplotype
snp
indel
3.9 years ago by
Parham
★ 1.6k
25
votes
15
replies
24k
views
7 follow
read.table does not read in all rows!
R
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Parham
★ 1.6k
1
vote
1
reply
1.7k
views
Biostar Handbook, student or professional?
handbook
student
professional
4.6 years ago by
Parham
★ 1.6k
1
vote
1
reply
1.7k
views
why sysID2product list for S. pombe is 2000 gene less than allnames list?
sysID2product
S.pombe
allnames
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
0
votes
1
reply
4.6k
views
What type of identifiers are GENE IDs of s. pombe to use in DAVID?
Gene-ID
DAVID
s.pombe
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Parham
★ 1.6k
5
votes
4
replies
1.5k
views
Making a data table more comprehensive
R
data.frame
transform
updated 7.4 years ago by
mikhail.shugay
3.5k • written 7.4 years ago by
Parham
★ 1.6k
5
votes
7
replies
6.0k
views
Rmarkdown report from multiple images
markdown
R
pandoc
knitr
updated 7.5 years ago by
ddiez
★ 2.0k • written 7.5 years ago by
Parham
★ 1.6k
5
votes
8
replies
12k
views
How to get geneID and not geneName from txdb made from a gff3 file?
gff3
txdb
genomicfeatures
pombe
pombase
updated 7.9 years ago by
uma
▴ 10 • written 7.9 years ago by
Parham
★ 1.6k
1
vote
4
replies
1.7k
views
Do you keep this batch or discard it?
RNA-Seq
RSeQC
geneBody_coverage
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Parham
★ 1.6k
10
votes
8
replies
15k
views
6 follow
Error for "gpar" while using pheatmap!
DESeq2
pheatmap
gpar
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Parham
★ 1.6k
1
vote
3
replies
2.3k
views
BED reference for Pombe
reference
bed
pombe
updated 2.4 years ago by
Ram
43k • written 8.5 years ago by
Parham
★ 1.6k
3
votes
4
replies
2.8k
views
problem with GTF for pombe
gtf
pombe
featurecounts
pombase
fission-yeast
updated 20 months ago by
Ram
43k • written 8.5 years ago by
Parham
★ 1.6k
2
votes
5
replies
1.5k
views
How to see if DEGs are grouped in genome?
overlap
DEG
rna-seq
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Parham
★ 1.6k
0
votes
1
reply
1.6k
views
How to prepare RNA-seq data for Piano?
piano
RNA-Seq
updated 17 months ago by
Ram
43k • written 8.8 years ago by
Parham
★ 1.6k
2
votes
3
replies
3.2k
views
Problem with extracting information from txdb object!
keytypes
txdb
updated 18 months ago by
Ram
43k • written 8.8 years ago by
Parham
★ 1.6k
1
vote
3
replies
2.2k
views
summarizeOverlap in systemPipeR not working!
summarizeoverlaps
systempiper
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Parham
★ 1.6k
30
votes
21
replies
6.7k
views
7 follow
Bash tutorial for biologists?
bash
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Parham
★ 1.6k
3
votes
2
replies
2.3k
views
Why goseq tutorial calculates median for gene length not sum?!
median
goseq
updated 22 months ago by
Ram
43k • written 9.0 years ago by
Parham
★ 1.6k
1
vote
2
replies
2.8k
views
Weird output when trying to convert sam to bam!
sam
samtools
bam
updated 24 months ago by
Ram
43k • written 9.2 years ago by
Parham
★ 1.6k
1
vote
2
replies
2.7k
views
Error in txdb workflow
r
select
txdb
updated 2.6 years ago by
Ram
43k • written 9.2 years ago by
Parham
★ 1.6k
3
votes
4
replies
2.8k
views
Error in systemPipeR
r
systemPipeR
updated 13 months ago by
Ram
43k • written 9.2 years ago by
Parham
★ 1.6k
6
votes
8
replies
3.0k
views
Why there are several different genes with exact same FPKM in the genes.fpkm_tracking of cuffdiff?
cuffdiff
fpkm
updated 2.3 years ago by
Ram
43k • written 9.2 years ago by
Parham
★ 1.6k
8
votes
6
replies
3.1k
views
How to split gene names in my list?
R
updated 2.1 years ago by
Ram
43k • written 9.2 years ago by
Parham
★ 1.6k
0
votes
2
replies
3.0k
views
How to merge replicates of mapped reads out of Tophat for pathview and gage analysis.
replicates
pathview
gage
Tophat
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Parham
★ 1.6k
4
votes
7
replies
5.9k
views
Is there any easy way to replicate R packages between two machines?
replicate
packages
R
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Parham
★ 1.6k
2
votes
5
replies
8.9k
views
Why Rstudio doesn't open scripts from projects when they are moved to a new machine?
R
projects
scripts
Rstudio
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Parham
★ 1.6k
1
vote
4
replies
1.8k
views
How to filter highly transcribed genes?
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
0
votes
0
replies
5.1k
views
Why numInCat are different from the number of GOs present in the list it is calculated from?
GO
numInCat
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
2
votes
3
replies
3.4k
views
How to do goseq with user created "lengthData" and category mapping objects?
gene.vector
lengthdata
goseq
category-mapping
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
3
votes
2
replies
3.3k
views
Two questions about plotting a venn diagram!
venn.diagram
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
3
votes
3
replies
2.5k
views
why do I get error for building txdb for S. pombe from biomart?
biomart
txdb
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
1
vote
2
replies
2.9k
views
How does heatmap in DESeq2 manual is helping the quality assessment?
DESeq2
Heatmap
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
2
votes
6
replies
5.3k
views
what does "Error: is(cds, "CountDataSet") is not TRUE" mean?
Error
DESeq2
varianceStabilizingTransformation
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
1
vote
0
replies
3.1k
views
What does the plots out of nullp and pwf mean?
goseq
nullp
pwf
plots
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
8
votes
1
reply
6.9k
views
How to see into a txdb object?
txdb
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
13
votes
16
replies
4.8k
views
How to equalize two vector lengths?
GO
vector length
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
1
vote
3
replies
5.0k
views
What is my RNA-seq data's library-type?!
RNA-seq
IGV
library-type
updated 3.1 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
4
votes
1
reply
1.7k
views
Why 2000 out of 7000 genes are not calculated?
RNA-seq
NAgenes
DESeq2
pombe
updated 3.1 years ago by
Ram
43k • written 9.5 years ago by
Parham
★ 1.6k
75 results • Page
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