soedinglab/BaMM_webserver

Issues

• The reported position of identified motif in the occurrence file does not seem to be accurate

  #150 opened a year ago by yasamanrezvani
  2

• [34036299] meme parser does not tolerate new line between motif definition and PWM

  #148 opened 5 years ago by croth1
  0

• [d84afd11]: need at least 2 points to select a bandwidth automatically

  #145 opened 5 years ago by croth1
  0

• [51e10f56] Error in if (strand_ind[i] == "+") {

  #142 opened 5 years ago by croth1
  1

• add textfield for sequence input

  #137 opened 6 years ago by croth1
  0

• make it clearer that uploaded files have to be raw text files

  #138 opened 6 years ago by croth1
  0

• BaMMScan allow searching sequences against a full database.

  #139 opened 6 years ago by croth1
  0

• [a5029173] bug in plotMotifDistribution.R

  #128 opened 6 years ago by wge11
  1

• [13809025] error in shoot-peng motif evaluation

  #129 opened 6 years ago by croth1
  1

• [62f6484c] bug in plotMotifDistribution.R

  #130 opened 6 years ago by wge11
  1

• add Drosophila database to our BaMM database

  #132 opened 6 years ago by wge11
  4

• [1b847ab3] unbound variable in pwm2bamm

  #134 opened 6 years ago by croth1
  0

• improve database text search

  #88 opened 6 years ago by croth1
  0

• export BaMMmatch results into a tsv/csv table file

  #131 opened 6 years ago by wge11
  0

• [f921038f] problem evaluating seeds

  #125 opened 6 years ago by croth1
  5

• fix calculation of probabilities in the left flanking region of the model

  #118 opened 6 years ago by wge11
  1

• 'utf-8' codec can't decode byte 0xd2 in position 16: invalid continuation byte

  #119 opened 6 years ago by croth1
  0

• Result page does not show images when FDR is not run

  #120 opened 6 years ago by croth1
  1

• [19530c7c] Error in plotBaMMLogo.R code

  #112 opened 6 years ago by wge11
  2

• Server does not stop updating when job crashes

  #113 opened 6 years ago by wge11
  2

• [edd271f9]: non-existing file error

  #114 opened 6 years ago by croth1
  2

• [9dd888d1] error in plotPvalStats.R

  #111 opened 6 years ago by croth1
  1

• [42c5d4b7] crash in MMcompare script

  #105 opened 6 years ago by croth1
  2

• [8c0cc6e9] segfault in FDR

  #98 opened 6 years ago by croth1
  1

• [1a38acd0] segfault in BaMM fdr

  #96 opened 6 years ago by croth1
  4

• [ffc51207] Problem with very short sequences

  #90 opened 6 years ago by croth1
  3

• Inconsistent databases

  #89 opened 6 years ago by croth1
  1

• [c05f7883] error raised in plotPvalStats.R

  #91 opened 6 years ago by croth1
  2

• [fa31e1f2] extra newlines in meme generated for refinement

  #93 opened 6 years ago by croth1
  1

• check all javascript for selecting motifs in manual denovo workflow broken

  #94 opened 6 years ago by croth1
  0

• visualize motif occurences in bammscan

  #42 opened 6 years ago by croth1
  4

• cleanup logic for jobs

  #44 opened 6 years ago by croth1
  1

• max. size of input file

  #87 opened 6 years ago by wge11
  0

• add full job_id to result pages

  #81 opened 6 years ago by croth1
  0

• bammscan: additionally show zeroth order of motif hits

  #47 opened 7 years ago by croth1
  0

• FDR evaluation: give scores for important fdr values

  #43 opened 6 years ago by croth1
  1

• reworking the motif database result page

  #68 opened 6 years ago by croth1
  0

• Roadmap to first revision

  #69 opened 6 years ago by croth1
  1

• testing the server workflows for revision 1

  #74 opened 6 years ago by croth1
  1

• making the webserver public

  #61 opened 6 years ago by croth1
  0

• Estimating the q from the data

  #65 opened 6 years ago by croth1
  3

• update performance plots on webserver

  #56 opened 6 years ago by croth1
  2

• Small post-submission bug-fixes

  #55 opened 6 years ago by croth1
  1

• fast FDR seeding

  #66 opened 6 years ago by croth1
  2

• Smaller example data

  #54 opened 7 years ago by croth1
  1

• upgrade to the latest peng version

  #39 opened 7 years ago by croth1
  1

• seeding workflow errors, when not at least one enriched motif found

  #49 opened 7 years ago by croth1
  1

• seeding workflow: selecting optimization fails when optimizing several times in a row.

  #50 opened 7 years ago by croth1
  0

• Remaining webserver issues

  #38 opened 7 years ago by mwess
  3

• testing and debugging new databases

  #41 opened 7 years ago by croth1
  2