Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Purecn
•
reset
0
votes
8
replies
1.5k
views
Error in running development version of PureCN
PureCN
software error
7.5 years ago
hustlxc
• 0
3
votes
5
replies
1.6k
views
Understanding PureCN and its germline SNPs
PureCN
germline
SNP
updated 5.9 years ago by
kakbrus
• 0 • written 6.1 years ago by
twtoal
▴ 10
0
votes
2
replies
1.1k
views
PureCN version clashes at GitHub and Bioconductor
version
PureCN
updated 4.4 years ago by
Mike Smith
★ 6.5k • written 4.4 years ago by
twtoal
▴ 10
0
votes
4
replies
1.3k
views
PureCN error: zero-length 'labels' specified
PureCN
6.0 years ago
twtoal
▴ 10
0
votes
2
replies
895
views
Mutation Burden file and manual curation
purecn
mutation_burden
manual_curation
5.6 years ago
twtoal
▴ 10
0
votes
9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
xiao.qiao.liu
• 0
1
vote
1
reply
941
views
PureCN support for indels
PureCN
indels
updated 6.1 years ago by
markus.riester
▴ 130 • written 6.1 years ago by
twtoal
▴ 10
0
votes
2
replies
976
views
No CNAs or SNVs in results
PureCN
6.0 years ago
twtoal
▴ 10
0
votes
1
reply
776
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
1
vote
1
reply
924
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 7.8 years ago by
markus.riester
▴ 130 • written 7.8 years ago by
klminch
▴ 10
0
votes
3
replies
970
views
PureCN warning: test.num.copy outside recommended range
PureCN
Warning
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
1
reply
1.8k
views
VCF file non-SNP germline mutations
PureCN
VCF
SNP
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
1
vote
3
replies
943
views
PureCN Release Notes
PureCN
Release
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
twtoal
▴ 10
0
votes
1
reply
978
views
coverage QC file mean duplication and "mom" columns
PureCN
coverage
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
4
replies
1.2k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN
Somatic Mutations
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
2
replies
1.3k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN
VCF
QUAL
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN
private_germline
mutation_burden
5.9 years ago
twtoal
▴ 10
0
votes
2
replies
866
views
PureCN removemapq0 parameter
PureCN
removemapq0
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
1
reply
953
views
Is C adjusted for purity?
PureCN
Adjusted C
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
5
replies
1.7k
views
Is mean adjusted for purity?
PureCN
mean ratio
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
2
replies
907
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
1
reply
683
views
Error in running example code of PureCN
PureCN
updated 7.5 years ago by
markus.riester
▴ 130 • written 7.5 years ago by
rahulk.aiims
• 0
0
votes
1
reply
951
views
how to make sure PureCN gets somatic status from VCF?
PureCN
updated 7.4 years ago by
markus.riester
▴ 130 • written 7.4 years ago by
eddieasalinas
• 0
2
votes
3
replies
1.2k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN
indel
somatic
germline
updated 6.9 years ago by
markus.riester
▴ 130 • written 6.9 years ago by
pathkim
• 0
0
votes
1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
xiao.qiao.liu
• 0
0
votes
1
reply
1.0k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.0 years ago by
markus.riester
▴ 130 • written 5.0 years ago by
twtoal
▴ 10
0
votes
3
replies
900
views
callLOH output file NA values
PureCN
NA values
updated 5.0 years ago by
markus.riester
▴ 130 • written 5.0 years ago by
twtoal
▴ 10
0
votes
1
reply
786
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN
CNV
CNA
segmentation
calculateTangentNormal
updated 4.4 years ago by
markus.riester
▴ 130 • written 4.4 years ago by
sruddy17
• 0
0
votes
4
replies
962
views
Why is PureCN LOH file missing some segments
purecn
loh
4.1 years ago
twtoal
▴ 10
0
votes
3
replies
1000
views
PureCN gene LOH very common, amp/del not
PureCN
gene
amplification
deletion
loh
updated 4.0 years ago by
markus.riester
▴ 130 • written 4.0 years ago by
twtoal
▴ 10
0
votes
1
reply
691
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation
GermlineMutation
PureCN
updated 2.7 years ago by
markus.riester
▴ 130 • written 2.7 years ago by
twtoal
▴ 10
0
votes
3
replies
859
views
Corrupt data in Sex column of .csv file
PureCN
3.0 years ago
twtoal
▴ 10
1
vote
8
replies
1.5k
views
PureCN: Copy Number of 7 issue
Pure
PureCN
updated 2.4 years ago by
markus.riester
▴ 130 • written 2.4 years ago by
jacobgross04
• 0
0
votes
2
replies
979
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN
COSMIC
updated 2.6 years ago by
markus.riester
▴ 130 • written 2.6 years ago by
twtoal
▴ 10
0
votes
3
replies
1.8k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.8 years ago • updated 5.7 years ago
twtoal
▴ 10
0
votes
4
replies
1.3k
views
PureCN optimum solution vs heat map
PureCN
Solution
Heatmap
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
1
vote
3
replies
1.0k
views
PureCN Manual Curation .rds file
PureCN
rds_file
manual_curation
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
0
votes
1
reply
740
views
PureCN PureCN.R --rds option recreate all output files?
PureCN
--rds
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
1
vote
1
reply
862
views
PureCN recover optimum solution
PureCN
Optimum_solution
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
0
votes
2
replies
1.1k
views
CNV in Normal Samples?
PureCN
Germline
Normal
CNV
updated 5.6 years ago by
markus.riester
▴ 130 • written 5.6 years ago by
twtoal
▴ 10
0
votes
1
reply
999
views
PureCN Solution Heatmap values
PureCN
heatmap
likelihoods
5.6 years ago
twtoal
▴ 10
0
votes
1
reply
998
views
Copy ratio threshold for calling actual CNV
PureCN
copy-ratio
threshold
updated 5.5 years ago by
markus.riester
▴ 130 • written 5.5 years ago by
twtoal
▴ 10
0
votes
3
replies
1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.5 years ago
twtoal
▴ 10
0
votes
1
reply
869
views
Copy ratio close to but not exactly 1
PureCN
CopyRatio
updated 5.5 years ago by
markus.riester
▴ 130 • written 5.5 years ago by
twtoal
▴ 10
0
votes
1
reply
871
views
Chromosome arm loss and --maxhomozygousloss default
Purecn
maxhomozygousloss
5.4 years ago
twtoal
▴ 10
0
votes
6
replies
1.7k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.9 years ago
skkujin
• 0
0
votes
1
reply
1.1k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.8 years ago
twtoal
▴ 10
0
votes
9
replies
1.6k
views
Unable to find solution: low coverage
PureCN
fatal error
no solution
5.9 years ago
twtoal
▴ 10
0
votes
2
replies
1.1k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN
ASCAT
purity
ploidy
multi-regional sequencing
3.8 years ago
twtoal
▴ 10
0
votes
4
replies
1.2k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN
Purity
Low Purity
CNV
5.9 years ago
twtoal
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Awards
• All
Teacher
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Scholar
to
ATpoint
★ 4.0k
Locations
• All
France,
18 minutes ago
Canada,
36 minutes ago
Japan,
40 minutes ago
San Diego,
42 minutes ago
United States,
57 minutes ago
Traffic: 735 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6