NCBI-Hackathons Scan2CNV issues

NCBI-Hackathons / Scan2CNV

MIT License

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Add option to normalize with all samples

#43 ekarlins opened 7 years ago
0
plan to read in idat files and normalize

#42 ekarlins opened 7 years ago
0
normalization in crlmm

#41 ekarlins opened 7 years ago
2
process idat files with R package gsrc

#40 ekarlins opened 7 years ago
17
CNV caller: DNAcopy

#39 ngiangre opened 7 years ago
2
CNV caller: VegaMC

#38 ngiangre opened 7 years ago
0
CNV caller: VEGA

#37 ngiangre opened 7 years ago
0
CNV caller: Copynumber

#36 ngiangre opened 7 years ago
0
CNV caller: biomvRhsmm

#35 ngiangre opened 7 years ago
0
CNV caller: gsrc

#34 ngiangre opened 7 years ago
0
CNV Caller: BirdSuite

#33 ngiangre closed 7 years ago
1
CNV Caller: QuantiSNP

#32 ngiangre opened 7 years ago
1
CNV Caller: PennCNV

#31 ngiangre opened 7 years ago
1
add "chr" to chromosome names in gsrc bed file

#30 ekarlins opened 7 years ago
6
check replicate concordance of CNV callers

#29 ekarlins opened 7 years ago
1
add other CNV callers

#28 ekarlins opened 7 years ago
4
run AutoConvert.exe on Windows command line

#27 ekarlins opened 7 years ago
0
teamlogo

#26 slsevilla closed 7 years ago
2
PennCNV Connection

#25 slsevilla closed 7 years ago
1
test bedtools to get intersection of multiple CNV callers

#24 ekarlins opened 7 years ago
4
test CNV calling in PennCNV

#23 ekarlins closed 7 years ago
1
R function to tell what bpm manifest was used to create an idat

#22 ekarlins opened 7 years ago
6
test scripts/ArrayScan2CNV.py

#21 ekarlins closed 7 years ago
16
help write the paper

#20 ekarlins opened 7 years ago
0
slides for presentation

#19 ekarlins closed 7 years ago
4
gtc2PennCNV error - Line 4 in <module>

#18 slsevilla closed 7 years ago
3
PennCNV HMM file

#17 ekarlins closed 7 years ago
2
PennCNV GC model file

#16 ekarlins closed 7 years ago
1
write snakefile to run pipeline

#15 ekarlins closed 7 years ago
1
run WINE and AutoConvert.exe to convert idat to gtc

#14 ekarlins opened 7 years ago
2
work on README

#13 ekarlins opened 7 years ago
10
generate PennCNV input txt files for all gtc files available

#12 ekarlins closed 7 years ago
2
generate PennCNV PFB file

#11 ekarlins closed 7 years ago
2
R code for cnv calling and plots using "gsrc"

#10 ekarlins closed 7 years ago
8
create a name and logo for our pipeline

#9 ekarlins closed 7 years ago
6
Tentative plan for creating gtc pipeline

#8 ekarlins closed 7 years ago
10
Tentative plan from the R side

#7 ngiangre closed 7 years ago
7
Error: cram package dependency RcppEigen

#6 ngiangre closed 7 years ago
0
python pipeline using gtc files

#5 ekarlins closed 7 years ago
2
R package for CNV calling from Illumina idats

#4 ekarlins closed 7 years ago
2
Two slides about project

#3 ekarlins closed 7 years ago
4
Sys admin

#2 ekarlins closed 7 years ago
2
Team writer

#1 ekarlins closed 7 years ago
2