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openCyto
•
reset
0
votes
0
replies
274
views
OpenCyto polyFunctions
openCyto
7 months ago
Albert
• 0
0
votes
0
replies
506
views
How to fix Flow-Data autoplot heat map
FlowCytometry
flowCore
openCyto
ggcyto
16 months ago
Dennis.hinkel
• 0
1
vote
1
reply
559
views
creating a NOT gate for gating out a single quadrant in a quadrant gate openCyto
FlowCytometry
Opencyto
updated 17 months ago by
Kevin Blighe
★ 3.9k • written 17 months ago by
Noël
• 0
0
votes
0
replies
407
views
gate_quad_sequential as parent gate for downstream gating in opencyto CSV template
opencyto
FlowCytometry
17 months ago
Noël
• 0
0
votes
0
replies
413
views
openCyto 2.8.0: error in prior_flowclust
prior_flowclust
openCyto
21 months ago
martin.andres
• 0
0
votes
2
replies
632
views
openCyto Problem: Registered Gating Function Executes Twice when Called
openCyto
register_plugins
gs_add_gating_method
3.8 years ago
geoffreylewen
• 0
0
votes
1
reply
639
views
FlowCore openCyto: problem with summary(result)
flowCore
openCyto
Summary
Result
Filter
updated 3.9 years ago by
Jake Wagner
▴ 310 • written 4.0 years ago by
noviello
• 0
7
votes
3
replies
1.2k
views
Adding quadGate.tmix to gating set with gs_pop_add
gs_pop_add
quadGate
openCyto
updated 3.9 years ago by
Jake Wagner
▴ 310 • written 3.9 years ago by
alavy
▴ 30
4
votes
5
replies
1.0k
views
Calculate F measure to compare different gating approaches for a specific cell population
flowWorkspace
flowCore
openCyto
flowFrame
F-measure
updated 3.9 years ago by
Jake Wagner
▴ 310 • written 4.0 years ago by
stefankolling+github
• 0
1
vote
5
replies
1.4k
views
custom gatingMethod not functioning / registering as expected (openCyto) (minDensity)
openCyto
registerPlugin
gatingMethod
minDensity
4.6 years ago
k.teijgeler
• 0
5
votes
11
replies
1.7k
views
polyFunctions gate in OpenCyto 1.20
opencyto
polyfunctions
polyfunctionsGate
updated 4.8 years ago by
Jiang, Mike
★ 1.3k • written 4.8 years ago by
k.teijgeler
• 0
0
votes
6
replies
1.4k
views
How to select left hand side of mindensity2 gate
openCyto
mindensity
updated 5.1 years ago by
Jiang, Mike
★ 1.3k • written 5.1 years ago by
biomiha
▴ 20
0
votes
7
replies
1.4k
views
RefGate populations switched in OpenCyto 1.20
RefGate
OpenCyto
updated 5.2 years ago by
Jiang, Mike
★ 1.3k • written 5.2 years ago by
k.teijgeler
• 0
3
votes
3
replies
1.7k
views
Opencyto - detector name not found in flow data, but pretty sure it's there
opencyto
flowcore
flow cytometry
updated 5.5 years ago by
Jiang, Mike
★ 1.3k • written 6.4 years ago by
Andrew Box
▴ 10
0
votes
4
replies
2.6k
views
Windows 10 openCyto Install: installation path not writeable, unable to update packages: boot, Matrix, mgcv
bioclite
openCyto
package installation
updated 6.1 years ago by
Jiang, Mike
★ 1.3k • written 6.5 years ago by
Robert Baer
▴ 70
0
votes
6
replies
1.6k
views
opencyto Error in .validity_check_alias
opencyto
updated 6.4 years ago by
Jiang, Mike
★ 1.3k • written 6.4 years ago by
biomiha
▴ 20
2
votes
5
replies
1.8k
views
How to find Geometric Mean from gated Quantibeads
flowworkspace
opencyto
updated 6.6 years ago by
Jiang, Mike
★ 1.3k • written 6.6 years ago by
justinyi10
▴ 10
1
vote
5
replies
1.9k
views
Measure Median Fluorescence Intensity in openCyto
opencyto
updated 6.7 years ago by
Jiang, Mike
★ 1.3k • written 6.7 years ago by
justinyi10
▴ 10
0
votes
1
reply
848
views
Fail to load openCyto
opencyto
bioconductor
updated 6.7 years ago by
Martin Morgan
25k • written 6.7 years ago by
justinyi10
▴ 10
0
votes
1
reply
2.5k
views
R Session Aborted; R ecountered a fatal error while loading openCyto
opencyto
fatal error
library
updated 6.7 years ago by
Jiang, Mike
★ 1.3k • written 6.7 years ago by
Maria
• 0
1
vote
1
reply
1.2k
views
Add flowclust gate to gatingset
opencyto
flowclust
updated 6.8 years ago by
Jiang, Mike
★ 1.3k • written 6.8 years ago by
pavitrarc
▴ 20
2
votes
1
reply
1.1k
views
openCyto displaying gating panels
opencyto
updated 7.2 years ago by
Jiang, Mike
★ 1.3k • written 7.2 years ago by
Rivka
• 0
2
votes
1
reply
981
views
openCyto working Example: expects {flowWorkspace} but example
opencyto
bioconductor
opencyto gating
updated 7.2 years ago by
Jiang, Mike
★ 1.3k • written 7.2 years ago by
Rivka
• 0
2
votes
4
replies
1.3k
views
Parsing flowWorkspace data
opencyto
R
flowworkspace
bioconductor
updated 7.3 years ago by
Jiang, Mike
★ 1.3k • written 7.3 years ago by
Rivka
• 0
1
vote
4
replies
1.4k
views
openCyto trouble importing xml file
opencyto
bioconductor
R
7.3 years ago
Rivka
• 0
0
votes
1
reply
1.2k
views
using flowIncubator package's function
opencyto
flow cytometry
R
package installation
updated 7.7 years ago by
Jiang, Mike
★ 1.3k • written 7.7 years ago by
anara92
• 0
1
vote
5
replies
1.8k
views
openCyto - flowclust.2d throws errors
opencyto
flow cytometry
updated 7.9 years ago by
bmuchmore
• 0 • written 7.9 years ago by
Ulrik Stervbo
▴ 30
0
votes
1
reply
2.1k
views
reading an ".xml" file as FlowJo Workspace file
opencyto gating
opencyto
flowcore
flowworkspace
updated 7.9 years ago by
Jiang, Mike
★ 1.3k • written 7.9 years ago by
anara92
• 0
1
vote
3
replies
1.3k
views
OpenCyto - getting gate coordinates
opencyto
7.9 years ago
Ulrik Stervbo
▴ 30
2
votes
1
reply
1.6k
views
Trouble parsing a workspace in flowWorkspace
flowworkspace
opencyto
updated 8.0 years ago by
lovetatting
▴ 10 • written 8.0 years ago by
wir.traumen
▴ 10
0
votes
1
reply
1.8k
views
FlowWorkspace and norm2Filter
flowcytometry
opencyto
flowworkspace
flowcore
8.0 years ago
Jiang, Mike
★ 1.3k
1
vote
2
replies
1.2k
views
openCyto - samples with low cell counts
flowcytometry
opencyto
8.2 years ago
Jiang, Mike
★ 1.3k
0
votes
3
replies
1.9k
views
openCyto: compilation failure during installation
opencyto
rhdf5
compilation error
8.2 years ago
gmirkin
• 0
1
vote
9
replies
3.1k
views
Problem with ggcyto/flowWorkspace from GitHub
software error
flowworkspace
opencyto
8.2 years ago
anders.tondell
▴ 30
4
votes
8
replies
2.7k
views
openCyto: usage and visualization of quadGate.tmix / collapsing data for flowClust
flowclust
opencyto
opencyto gating
updated 8.3 years ago by
Greg Finak
▴ 240 • written 8.4 years ago by
Viktor Thiel
• 0
0
votes
5
replies
1.9k
views
openCyto fails to load
opencyto
bioclite
updated 8.4 years ago by
yang.chen
• 0 • written 8.4 years ago by
pavitrarc
▴ 20
0
votes
4
replies
1.6k
views
Issues parsing workspace in openCyto
opencyto
8.7 years ago
JK
▴ 10
0
votes
0
replies
1.4k
views
openCyto transitional gate
flow cytometry
opencyto
8.9 years ago
Jiang, Mike
★ 1.3k
0
votes
0
replies
1.3k
views
Re: FlowStats help
flowclust
opencyto
flowcytometry
9.0 years ago
Jiang, Mike
★ 1.3k
5
votes
4
replies
3.0k
views
openCyto: Using combination gates (boolean gates)
opencyto
opencyto gating
FlowJo
updated 9.2 years ago by
Greg Finak
▴ 150 • written 9.2 years ago by
juancamilos
▴ 10
4
votes
1
reply
1.6k
views
News:
New Flow Cytometry Data Analysis Framework
flowcore
flowcytometry
opencyto
new
News
9.5 years ago
Greg Finak
▴ 150
1
vote
0
replies
1.7k
views
Issue with flowDensity on OpenCyto
flowClust
openCyto
flowDensity
flowClust
openCyto
flowDensity
9.6 years ago
Jiang, Mike
★ 1.3k
0
votes
1
reply
1.4k
views
OpenCyto
Cancer
eisa
openCyto
Cancer
eisa
openCyto
9.8 years ago • updated 9.7 years ago
Jiang, Mike
★ 1.3k
0
votes
0
replies
897
views
Bioconductor Digest, Vol 134, Issue 10
openCyto
flowDensity
openCyto
flowDensity
9.9 years ago
Jiang, Mike
★ 1.3k
44 results • Page
1 of 1
Recent ...
Replies
Comment: DEG Filtering
by
Amit
• 0
Hello Gordon, The PCA plot for RMA normalized data shows Mixing of samples. Is it Batch Effect ? Because when I apply ARSyNseq() and again …
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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50k
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