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smithlabcode
/
methpipe
A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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size of HMRs from RRBS compared to WGBS
#229
farmohh
closed
1 year ago
0
bismark deduplicated BAM
#228
biozzq
closed
1 year ago
2
hmr should not check for alphabetical ordering of chromosomes
#226
guilhermesena1
closed
2 years ago
1
Radmeth reporting whole genome as DMR
#221
guilhermesena1
closed
2 years ago
1
Reading files of methylation levels
#216
andrewdavidsmith
closed
1 year ago
1
format_reads for bwa-meth's SAM files
#215
diegommcc
closed
1 year ago
1
methstates doesn't read FASTA files with multiple chromosomes
#212
guilhermesena1
closed
2 years ago
1
Update methpipe-manual.tex
#211
hchetia
closed
2 years ago
1
Install failure, any suggestion?
#210
ShixiangWang
closed
2 years ago
2
Getting started with amrtester
#209
ctsa
closed
2 years ago
0
Using radmeth to call DMRs
#207
vagan21
closed
1 year ago
4
5mC and 5hmC tracks
#206
hchetia
closed
2 years ago
0
radmeth adjust - "Core Dumped"
#204
Mazklaus
closed
1 year ago
2
MAPQ filtering
#203
vagan21
closed
1 year ago
1
format_reads and mapping
#202
vagan21
closed
2 years ago
2
optimizing pipeline (especially speed)
#201
moqri
closed
1 year ago
3
NULL lines contained in .mr file which transformed from bam file
#197
vanessayang0927
closed
2 years ago
3
bigWig_to_methcounts --missing file or installation step.
#196
Blosberg
closed
2 years ago
4
hmr fails on sorted CpG's
#195
cb4github
closed
2 years ago
4
Installation issue htslib/sam.h
#194
simiro
closed
2 years ago
3
Install fatal error: gsl/gsl_sf_psi.h
#193
avkermanov
closed
2 years ago
4
Using Nanopore data
#192
Hannah1746
closed
2 years ago
2
Documentation for fast-liftover tool
#191
andrewdavidsmith
closed
2 years ago
1
average 5hmC and true 5mC level in regions of interest?
#190
BenvanderVeer
closed
2 years ago
2
Install fatal error: gsl/gsl_sf_psi.h: No such file or directory
#189
Hannah1746
closed
2 years ago
15
problem with installing methpipe on HPC server
#188
BenvanderVeer
closed
3 years ago
5
meth to bed
#187
hchetia
closed
3 years ago
2
Error running hmr program on symmetric cpgs
#186
hchetia
closed
3 years ago
33
Issue with mlml: `error: chrom or pos mismatch in both files`
#185
PanZiwei
closed
3 years ago
4
Error "chromosome in SAM file not found in reference:chr1"
#184
hchetia
closed
3 years ago
8
incompatible behavior between abismal and methpipe with chrom names
#183
guilhermesena1
closed
3 years ago
1
Failing to do recursive configuration for sam_pre_release branch
#182
andrewdavidsmith
closed
3 years ago
4
Submodule in detached head state
#181
andrewdavidsmith
closed
3 years ago
2
Problem building with original Makefiles
#180
andrewdavidsmith
closed
3 years ago
3
Memory Error when calling pmd
#179
shashwatsahay
closed
1 year ago
5
Issue with mlml
#178
mariazanti
closed
2 years ago
2
Methcounts: problem with chrom order in mapped reads
#177
shashwatsahay
closed
3 years ago
3
Problem with methcounts!
#176
cheehowteo
closed
2 years ago
2
How are you defining a hypomethylated region numerically?
#175
vagan21
closed
3 years ago
1
MethPipe ASM score query
#174
kashiff007
closed
1 year ago
2
to-mr cannot transform successfully instead of generating a null .mr file
#173
xxzzwan
closed
3 years ago
4
”bad line in MappedRead file” when using bsrate function
#172
xxzzwan
closed
3 years ago
6
Sam pre release
#171
SDeans0
closed
3 years ago
1
Assigning of reads into um: unmethylated-methylated and mu: methylated-unmethylated to its alleles by 'allelicmeth'
#170
kashiff007
closed
3 years ago
5
compilation with gcc 10
#169
hchetia
closed
3 years ago
3
"hmr_plant" absent
#168
hchetia
closed
3 years ago
3
Error running hmr & pmd
#167
hchetia
closed
3 years ago
5
Error with test dataset
#166
hchetia
closed
3 years ago
6
Question about design matrix
#165
eribue
closed
1 year ago
2
Unable to make & make install
#164
hchetia
closed
3 years ago
14
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