Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / EI-CoreBioinformatics/mikado issues and pull requests

#462 - Remove Anaconda packages from defaults channel

Issue - State: open - Opened by gq1 12 days ago - 1 comment

#461 - documentation :: some comments

Issue - State: open - Opened by EricDeveaud 3 months ago

#460 - self_training.py :: missing scikit-learn

Issue - State: open - Opened by EricDeveaud 3 months ago

#459 - Transcript sources and isoforms

Issue - State: open - Opened by 14zac2 4 months ago

#456 - Fix/gh workflows

Pull Request - State: closed - Opened by gemygk 9 months ago

#455 - Mikado pick does't add the CDS

Issue - State: open - Opened by francicco 9 months ago

#454 - Bump scipy from 1.9.2 to 1.11.1

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 4 comments
Labels: dependencies

#453 - fix: pin mikado python dependencies

Pull Request - State: closed - Opened by gemygk 9 months ago - 12 comments

#452 - Assign transcripts to loci

Issue - State: open - Opened by francicco 10 months ago

#451 - Error in mikado conda

Issue - State: open - Opened by edugenetico 10 months ago

#450 - Error with mikado serialise: 'Engine' object has no attribute 'cursor'

Issue - State: open - Opened by bbista 12 months ago - 4 comments

#449 - Error in rule asm_gff_stats

Issue - State: open - Opened by jwli-code about 1 year ago

#448 - can't install Mikado by different ways

Issue - State: open - Opened by mezoderma about 1 year ago - 1 comment

#447 - Parameters to avoid overlap

Issue - State: open - Opened by xiekunwhy over 1 year ago

#446 - Optimising Scoring file

Issue - State: closed - Opened by francicco over 1 year ago - 12 comments

#445 - Unable to install mikado with mamba via multiple strategies

Issue - State: open - Opened by isaacvock over 1 year ago - 4 comments

#444 - scipy._build_utils is no longer available in scipy 1.10+

Issue - State: open - Opened by boegel over 1 year ago

#443 - fix: pip install mikado now works

Pull Request - State: closed - Opened by MmasterT over 1 year ago - 1 comment

#442 - Error running serialise

Issue - State: open - Opened by johannesnicolaus over 1 year ago - 1 comment

#441 - Track gene/transcript ids

Issue - State: open - Opened by francicco almost 2 years ago

#439 - Comparing two annotations

Issue - State: open - Opened by AlexdeMendoza almost 2 years ago - 1 comment

#438 - error with running mikado

Issue - State: closed - Opened by ChemaMD almost 2 years ago - 3 comments

#437 - configuration error with mikado 2.3.2

Issue - State: open - Opened by baozg about 2 years ago - 1 comment

#436 - Designing specific scoring file

Issue - State: open - Opened by allind over 2 years ago - 1 comment

#435 - Best practice to use Mikado to score assembled lncRNA

Issue - State: open - Opened by cc-prolix over 2 years ago - 3 comments

#434 - Issue #433 - changing the order of operations in printing out the fil…

Pull Request - State: closed - Opened by lucventurini over 2 years ago - 3 comments

#433 - Update requirements.txt

Pull Request - State: closed - Opened by ljyanesm over 2 years ago - 5 comments

#432 - Mikado crashed, cause: unhashable type: 'list'

Issue - State: closed - Opened by dadrasarmin over 2 years ago - 2 comments

#431 - Configuration.yaml is empty

Issue - State: closed - Opened by bbista over 2 years ago - 3 comments

#430 - Mikado and PASA+EVM

Issue - State: closed - Opened by sanyalab almost 3 years ago - 1 comment

#429 - Mikado serialise sql3 error

Issue - State: closed - Opened by AlexdeMendoza almost 3 years ago - 3 comments

#428 - Is there a way to update all transcript to complete gene models?

Issue - State: closed - Opened by xiekunwhy almost 3 years ago - 2 comments

#427 - How to keep CDS information in input gtf files?

Issue - State: closed - Opened by xiekunwhy about 3 years ago - 6 comments

#426 - Allow codon table to be set in mikado prepare

Issue - State: closed - Opened by swarbred about 3 years ago - 3 comments

#425 - Merge bams or each bam separately?

Issue - State: closed - Opened by xiekunwhy about 3 years ago - 5 comments

#424 - OSError: [Errno 27] File too large

Issue - State: closed - Opened by NJeanray over 3 years ago

#423 - HSP uniqueness could fail in rare cases

Pull Request - State: closed - Opened by ljyanesm over 3 years ago - 1 comment

#422 - sqlite3.IntegrityError during mikado serialise with blast homology

Issue - State: closed - Opened by JulienPPichon over 3 years ago - 21 comments

#421 - Trinity doesn't give me any results

Issue - State: closed - Opened by NJeanray over 3 years ago - 3 comments

#420 - Fix issue with empty blast results in tsv format

Pull Request - State: closed - Opened by ljyanesm over 3 years ago

#419 - Solve performance issues affecting extra-dense superloci in ONT runs.

Pull Request - State: closed - Opened by lucventurini over 3 years ago - 1 comment

#418 - Bulk add transcripts method

Pull Request - State: closed - Opened by lucventurini over 3 years ago - 1 comment

#417 - [main_samview] fail to read the header from "-".

Issue - State: closed - Opened by NJeanray over 3 years ago - 4 comments

#416 - Mikado using STAR : limitGenomeGenerateRAM

Issue - State: closed - Opened by NJeanray over 3 years ago - 4 comments

#415 - mikdo pick throws this error and results in very few transcripts

Issue - State: closed - Opened by aseetharam over 3 years ago - 12 comments
Labels: bug

#414 - Using mikado to correct MAKER CDS sequences.

Issue - State: closed - Opened by keithforestdecker over 3 years ago - 2 comments

#413 - Prepare bug with lowercase bases

Issue - State: closed - Opened by swarbred over 3 years ago

#412 - Testing the installed module UnicodeDecodeError

Issue - State: closed - Opened by bismarck1008 over 3 years ago - 1 comment

#411 - bug in transcriptchecker.py at line 255

Issue - State: closed - Opened by cooketho over 3 years ago - 3 comments

#410 - Missing coding regions

Issue - State: closed - Opened by francicco over 3 years ago - 16 comments

#409 - 'list' object has no attribute 'finalize'

Issue - State: closed - Opened by francicco over 3 years ago - 2 comments

#408 - Minor fixes

Pull Request - State: closed - Opened by ljyanesm over 3 years ago - 1 comment

#407 - WIP - mikado-405 Remove UTRs

Pull Request - State: closed - Opened by ljyanesm over 3 years ago

#406 - Issue 404 extract promoter

Pull Request - State: closed - Opened by ljyanesm over 3 years ago

#405 - Remove UTRs

Issue - State: closed - Opened by homonecloco over 3 years ago - 2 comments

#404 - Error with logger on exptract_promoter

Issue - State: closed - Opened by homonecloco over 3 years ago - 2 comments

#403 - CAT to Mikado

Issue - State: closed - Opened by francicco almost 4 years ago - 8 comments

#402 - Issue 401 daijin class2

Pull Request - State: closed - Opened by ljyanesm almost 4 years ago - 1 comment

#401 - Cannot run Class2 in Daijin pipeline

Issue - State: closed - Opened by louphey almost 4 years ago - 3 comments

#400 - Version 2.2.4

Pull Request - State: closed - Opened by lucventurini almost 4 years ago - 2 comments

#399 - Fixed GHA

Pull Request - State: closed - Opened by lucventurini almost 4 years ago

#398 - Error in rule uncompress_genome

Issue - State: closed - Opened by louphey almost 4 years ago - 2 comments
Labels: bug

#397 - Error in rule mikado_prepare

Issue - State: closed - Opened by louphey almost 4 years ago - 3 comments

#395 - [BUG] Mikado crashes due to a bug in padding

Issue - State: closed - Opened by lucventurini almost 4 years ago - 1 comment
Labels: bug, EI-Internal

#394 - Question about using Mikado with lncRNA annotations.

Issue - State: closed - Opened by cc-prolix almost 4 years ago - 2 comments
Labels: question

#393 - Issue 392

Pull Request - State: closed - Opened by lucventurini almost 4 years ago

#392 - serialise fails to load blast dbase .. can't find entries ... dictionary value error issue

Issue - State: closed - Opened by adamfreedman almost 4 years ago - 13 comments
Labels: bug, question

#391 - Repeat sequences in genome

Issue - State: closed - Opened by wyim-pgl almost 4 years ago - 1 comment
Labels: enhancement, question

#390 - Version 2.2.2

Pull Request - State: closed - Opened by lucventurini almost 4 years ago - 1 comment

#389 - Output BED12 rather than GTF from Mikado prepare

Issue - State: closed - Opened by lucventurini almost 4 years ago
Labels: enhancement, EI-Internal

#388 - Make mikado compatible with Sqlalchemy 1.4.0 and following

Issue - State: closed - Opened by lucventurini almost 4 years ago - 3 comments
Labels: enhancement, EI-Internal

#387 - Seed is not constant between runs with seed = 0

Issue - State: closed - Opened by gemygk almost 4 years ago - 1 comment

#385 - missing explaination of mikado.bed in tutorial

Issue - State: closed - Opened by cooketho almost 4 years ago - 2 comments
Labels: enhancement, question, EI-Internal

#384 - mkado util convert - additional gene lines

Issue - State: closed - Opened by swarbred almost 4 years ago - 4 comments
Labels: enhancement

#383 - Fix v2.1.2

Pull Request - State: closed - Opened by lucventurini almost 4 years ago - 1 comment

#382 - Have Mikado serialise scoop the junction coordinates from the block_size/block_starts

Issue - State: closed - Opened by lucventurini almost 4 years ago
Labels: enhancement

#381 - Mikado prepare freezes if one of the input files has the wrong extension

Issue - State: closed - Opened by lucventurini almost 4 years ago
Labels: bug

#380 - Readying for 2.1.1, see CHANGELOG.

Pull Request - State: closed - Opened by lucventurini almost 4 years ago - 2 comments

#379 - Issue 375

Pull Request - State: closed - Opened by lucventurini almost 4 years ago - 3 comments
Labels: enhancement

#378 - Add "." for unstranded models in mikado util stats --tab-stats output

Issue - State: closed - Opened by swarbred almost 4 years ago - 1 comment
Labels: enhancement

#377 - Issue 376

Pull Request - State: closed - Opened by lucventurini about 4 years ago

#376 - IndexError in Mikado Serialise

Issue - State: closed - Opened by lukesarre about 4 years ago - 10 comments

#375 - [Future enhancement] Switch networkx with igraph or networkit

Issue - State: closed - Opened by lucventurini about 4 years ago
Labels: enhancement, EI-Internal

#374 - Hotfix pick

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 1 comment

#372 - Fix configure

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 2 comments

#371 - Issue 136

Pull Request - State: closed - Opened by lucventurini about 4 years ago

#370 - Issue 368 marshmallow

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 2 comments

#369 - Issue 368 configure validation

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 2 comments

#368 - Mikado configure should only allow options in validation blueprint

Issue - State: closed - Opened by ljyanesm about 4 years ago - 6 comments

#367 - Make sure there are enough values in row

Pull Request - State: closed - Opened by ljyanesm about 4 years ago

#366 - Issue 307 multiorf metrics

Pull Request - State: closed - Opened by lucventurini about 4 years ago

#365 - Revised error messages

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 1 comment

#364 - Issue 353

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 1 comment

#363 - Issue 362 gh actions

Pull Request - State: closed - Opened by lucventurini about 4 years ago - 1 comment
Labels: enhancement, EI-Internal

#362 - Move from Travis CI to GitHub actions

Issue - State: closed - Opened by lucventurini about 4 years ago
Labels: EI-Internal

#361 - Let Mikado prepare generate a custom label if none provided

Issue - State: closed - Opened by lucventurini about 4 years ago - 1 comment
Labels: enhancement, EI-Internal