yupenghe/methylpy

Issues

• No @RG in bam files, so Picard cannot MergeDuplicates

  #95 opened 2 months ago by markram4
  0

• DMRfind generates thousands of chunk.tsv files

  #94 opened 4 months ago by MeganAdler
  1

• The result of DMRfind seem to be few compared with bw in IGV

  #93 opened 4 months ago by liyangyang12
  0

• Call DMR using files in 10 bp bin format

  #91 opened 7 months ago by Greacy-x
  6

• Issue with Methylpy Single-End-Pipeline Using “–pbat True”

  #92 opened 6 months ago by riverwin1207
  1

• methylpy 1.4.7

  #90 opened 8 months ago by liyangyang12
  3

• Run DMRfind failed

  #89 opened 10 months ago by DingWB
  7

• methylpy single-end-pipeline error

  #88 opened a year ago by hengbingao
  2

• methylpy call-methylation-state

  #87 opened a year ago by MagdalenaWinklhofer
  9

• Double free or corruption error when running run_test.py

  #86 opened a year ago by XunuoZhu
  1

• running reidentify-DMR on the DMRfind results

  #85 opened 2 years ago by FarzanehRah
  6

• Low percentage of uniquely mapping read pairs

  #46 opened 2 years ago by GatorShan
  7

• CpG

  #84 opened 2 years ago by ShouWenWang
  1

• methylpy has took long time.

  #83 opened 2 years ago by Biomamba
  2

• how to acquire or calculate the mapping efficiency using methylpy?

  #82 opened 2 years ago by InfiniteLaugh
  3

• low align rate conflicting with bismark align rate

  #81 opened 2 years ago by yinzhuo0322
  4

• binom-test failed

  #78 opened 2 years ago by Davieni4yashiro
  15

• NAs of methylpy add-methylation-level result

  #80 opened 2 years ago by liyangyang12
  5

• DMRfind-Histogram FDR correction did not converge.

  #79 opened 2 years ago by nnlrl
  1

• DMR

  #77 opened 2 years ago by liyangyang12
  4

• Methylpy in plant

  #76 opened 3 years ago by zzh4399
  7

• mapping to a large genome

  #75 opened 3 years ago by awieeeee
  1

• Help for parameters tuning.

  #74 opened 3 years ago by ifishlin
  0

• Methylation calling in non-directional libraries

  #73 opened 3 years ago by rbpisupati
  1

• bam-quality-filter NOMe-seq

  #72 opened 3 years ago by sherryxuePKU
  2

• Ubuntu Optional step to Compile rms.cpp is formatted wrong

  #71 opened 3 years ago by adioni
  1

• Running RMS tests failed.

  #70 opened 4 years ago by chenji333
  18

• cutadapt error for methylpy v 1.4.6

  #69 opened 4 years ago by shahsam
  3

• run_test.py fails

  #68 opened 4 years ago by rungitta
  21

• DMRfinnd RMS issue

  #49 opened 4 years ago by Papareddy
  2

• Where is the methylation difference reflected in the DMRfind code

  #65 opened 4 years ago by BTSARMY0613
  11

• Methylpy and Bismark for alignment

  #64 opened 4 years ago by shengyongniu
  0

• DMRfind - Histogram FDR correction did not converge

  #58 opened 4 years ago by connorrogerson
  1

• Average methylation level of a sample

  #66 opened 4 years ago by connorrogerson
  1

• DMRfind fails with key error 179

  #67 opened 4 years ago by georgback
  2

• multi-threading indexing?

  #62 opened 4 years ago by yvnkm
  4

• DMRfind use two samples is ok but a lot of samples is wrong

  #63 opened 4 years ago by BTSARMY0613
  24

• methylpy add-methylation-level issue

  #53 opened 4 years ago by coralzhang
  15

• multiple core problems

  #61 opened 4 years ago by coralzhang
  4

• PATH to Picard

  #60 opened 4 years ago by olmath
  1

• DMRfind Running RMS tests failed.

  #59 opened 4 years ago by BTSARMY0613
  5

• add-methylation-level issue

  #57 opened 5 years ago by WWJiaxuan
  6

• default DMRfind --dmr_max_dist

  #55 opened 5 years ago by shellywanamaker
  2

• DMRfind with multiple repeats

  #56 opened 5 years ago by coralzhang
  5

• output file by add-methylation-level

  #54 opened 5 years ago by WWJiaxuan
  1

• add-methylation level not working

  #48 opened 5 years ago by knoedlerj
  12

• input files for add-methylation-level

  #51 opened 5 years ago by WWJiaxuan
  9

• why are some regions with >= min_num_dms not called DMRs?

  #52 opened 5 years ago by shellywanamaker
  4

• DMRfind error during merging DMS to DMR

  #50 opened 5 years ago by shahsam
  5

• rms ValueError: could not convert string to float

  #45 opened 5 years ago by shellywanamaker
  2