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smithlabcode
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methpipe
A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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expected class-name before ‘(’ token SMITHLABException
#163
Myskiper
closed
3 years ago
5
methcounts_sam not processing chr10 in a sample
#162
terencewtli
closed
4 years ago
1
Problem when running methcounts, pmd, etc!
#161
bobia9991
closed
1 year ago
4
duplicate-remover_sam must do the sorting based on end coordinate
#160
guilhermesena1
closed
4 years ago
1
duplicate-remover_sam not running when args are provided according to OptionParser
#159
guilhermesena1
closed
4 years ago
1
mac warning in TwoStateHMM_PMD.cpp
#158
terencewtli
closed
3 years ago
1
format_reads too slow
#157
andrewdavidsmith
closed
3 years ago
1
bsrate_sam takes a long time if input has random chrom distribution
#156
guilhermesena1
closed
4 years ago
3
duplicate-remover: include information from SAM header
#155
terencewtli
closed
4 years ago
1
Incomplete files
#154
surak
closed
4 years ago
1
methcounts reporting no reads for a chrom when chroms are missing
#153
andrewdavidsmith
closed
3 years ago
2
Methylation level calculation for PMD
#152
juheon
closed
4 years ago
2
Where is headers within libsmithlab_cpp-1.0.2?
#151
aganve
closed
3 years ago
1
tar.gz file
#150
lauzikaite
closed
4 years ago
2
mlml error mlml:cpp:244:void expectation....
#149
grrompala
closed
4 years ago
1
to-mr program for bsmap
#147
jinsooahn
closed
3 years ago
1
Reading in symmetric CpGs into hmr
#146
tsengale
closed
4 years ago
2
methdiff output format: inconsistency between coverage and methylated read counts
#145
akmorrow13
closed
4 years ago
5
MLML problems
#144
soleilll
closed
4 years ago
5
Unsynchronized update of parameters
#143
xjlizji
closed
1 year ago
2
merge-methcounts split the same sites into different rows
#142
yongchao
closed
5 years ago
10
hmr rep passing vectors by const value?
#141
andrewdavidsmith
closed
5 years ago
3
hmr rep passing vectors by const value?
#140
andrewdavidsmith
closed
5 years ago
0
GZ support
#139
mengzhou
closed
5 years ago
0
[Cleanup TwoStatHMM.*pp] Function declarations include non-const, non-reference primitive types?
#138
andrewdavidsmith
closed
5 years ago
6
merge-methcounts producing massive file size is normal?
#137
Surajuvm
closed
5 years ago
5
Behavior of methcounts when chroms missing from mapped read files
#136
andrewdavidsmith
closed
5 years ago
2
Read gzip compressed .sam or .mr files for input
#135
enormandeau
closed
5 years ago
2
to-mr extremely slow?
#134
sirselim
closed
5 years ago
1
struct Site in merge-methcounts.cpp
#133
masarunakajima
closed
5 years ago
1
duplicate-remover stats fix
#132
mengzhou
closed
5 years ago
1
Segmentation fault in to-mr with some SAM files
#131
cviner
closed
5 years ago
3
Changed the output format of the levels program
#130
andrewdavidsmith
closed
6 years ago
0
HMR score column larger than 1000, error from bedToBigBed
#129
jdnukem
closed
6 years ago
2
duplicate remover summary statistics augmentation
#128
andrewdavidsmith
closed
5 years ago
1
Minor: methcounts -about doesn't work
#127
slockton
closed
5 years ago
1
Output format of methdiff and radmeth is not consistent
#126
mengzhou
closed
1 year ago
2
Score displaying only `+` in radmeth merge output
#125
martinjvickers
closed
5 years ago
2
MLML documentation missing from Methpipe
#124
jqujqu
closed
3 years ago
4
Input file validation for merge-methcounts
#123
martinjvickers
closed
6 years ago
1
Use of is_methpipe_file_single causes loss of the first line
#122
mengzhou
closed
6 years ago
1
Replacing smithlab_exceptions with std::runtime_error()
#121
sarahsma
closed
5 years ago
1
GCC
#120
hmyh1202
closed
5 years ago
4
duplicate-remover error "input not properly sorted" with paired end reads
#119
aimstar2006
closed
6 years ago
2
Methcounts not working properly
#118
yangliyan1991
closed
5 years ago
8
How to compare amr in different groups
#117
wkl1990
closed
5 years ago
8
Add mlml option to output methcount file for the indirectly profiled mark
#116
jqujqu
closed
6 years ago
1
p-values and counting methylated sites in DMR
#115
martinjvickers
closed
6 years ago
3
Question for method of ASM calling
#114
hmyh1202
closed
6 years ago
1
Question?
#113
hmyh1202
closed
6 years ago
2
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