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Devon Ryan dpryan79 Genedata AG Basel, Switzerland / Freiburg, Germany Neuroscientist/ion channel biophysicist turned bioinformatician.

deeptools/pyGenomeTracks 525

python module to plot beautiful and highly customizable genome browser tracks

deeptools/deepTools 493

Tools to process and analyze deep sequencing data.

dpryan79/ChromosomeMappings 194

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

deeptools/pyBigWig 143

A python extension for quick access to bigWig and bigBed files

alex-rudakov/sphinx-argparse 48

Sphinx extension that automatically document argparse commands and options

deeptools/py2bit 11

A python library for accessing 2bit files

dpryan79/bison 8

Bisulfite alignment on nodes of a cluster

dpryan79/Answers 7

Random code produced to answer questions on biostars/seqanswers/etc.

dpryan79/BBMeth 3

BBMeth: An R package for fitting methylation data with a beta-binomial model

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Jake Lehle

commit sha dffb6050d3c0d56183b851a1cc666c04912a7f78

bump/gembs (#32436) * bump/gembs An offering to our science overlords. * Why do I hope? * Fools rush in * This will work I swear

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bump/gembs

An offering to our science overlords.

Bump gemBS to version 3.5.1.

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Bioconda Bot

commit sha e6c4c065fc60227869c95b9f1e4ff97453506a5a

Update ncbimeta to 0.8.3 (#32396) * Update ncbimeta to 0.8.3 * ncbimeta: update python, biopython, and numpy dependencies Co-authored-by: Katherine Eaton <ktmeaton@gmail.com>

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Felix Mölder

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update blast (#32386)

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Update vsearch to 2.21.0 (#32388)

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Update pango-designation to 1.2.123 (#32397)

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Michael Steinbaugh

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Update mashmap (to fix build on macOS) (#32385) * Need to add mkl for macOS * Need to remove mashmap from denylist

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Mikko Rautiainen

commit sha 2f1195d5249f10f8df7c7fa6cd608b05050548ba

Try to trigger GraphAligner package build (#32392) * Try to trigger packaging by increasing build number * remove GraphAligner from build blacklist * Build number back to 0 * use old version of boost which has serialization and program options * add libboost too

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Bioconda Bot

commit sha 961918f6602c89ec107981c76110724407ae5244

Update parsnp to 1.6.0 (#32345) * Update parsnp to 1.6.0 * Update meta.yaml * Update meta.yaml * Skip osx again Co-authored-by: Bryce Kille <brycekille@gmail.com> Co-authored-by: Andreas Sjödin <andreas.sjodin@gmail.com>

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Bioconda Bot

commit sha 01df63efafdb5abbfdd4899d8633755349975793

Update parascopy to 1.3.2 (#32399)

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zhenxian

commit sha 9fdab5297d408402d6865aca20ef4d113112a232

update version to v0.1.10 (#32403)

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Bioconda Bot

commit sha 2bb66fa909b585be000b38b9a44f815a4e037dbf

Update fwdpy11 to 0.17.1 (#32400)

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Bioconda Bot

commit sha 470a1ed57c805331e55946740f8a76a2ed69082f

Update gfapy to 1.2.2 (#32401)

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Pedro Queirós

commit sha 077bfb7cea5456badd2ec67a434ea2f6acb27eab

update mantis_pfa recipe (#32406) * update mantis_pfa recipe * update recipe

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Ed Harry

commit sha 1e00795fd629e7a42b4944cd0bab4dae8e092b3e

add linkstats (#32389) * add linkstats * add linkstats * add linkstats * add linkstats * add linkstats * add linkstats * add linkstats * Update meta.yaml * add linkstats * add linkstats * add linkstats * add linkstats * Update meta.yaml Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>

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Bioconda Bot

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Update bifrost to 1.0.6 (#32402)

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Update thapbi-pict to 0.11.0 (#32405)

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Update diamond to 2.0.14 (#32404)

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Update dropseq_tools to 2.5.1 (#32407)

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Update cellrank to 1.5.1 (#32408)

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Update ataqv to 1.3.0 (#32411)

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Devon Ryan

commit sha 10bc78736927a1680ba7d1cffd5f8ea64f30d710

Add missing patches

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Mike Cormier

commit sha b760f349d8399a11d35a7d0ffe8afbdec2c82c96

Add ConSplice bioconda recipe (#32432) * ConSplice bioconda recipe * Fix name * fix package issue * Fix os error * Test config * update sha256 * Update sha256 * check post-link * test * Update sha256 * Update sha256 * Update sha256 * Update sha256 * Update sha256 * Update sha256 * Update sha256

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PR merged bioconda/bioconda-recipes

Add ConSplice bioconda recipe please review & merge

Describe your pull request here

Add a new bioconda recipe for the ConSplice project.

ConSplice models that splicing constraint in the human genome and provides a splice-altering pathogenic score for each variant in protein-coding genes.


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
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<table> <tr> <td><code>@BiocondaBot please update</code></td> <td>Merge the master branch into a PR.</td> </tr> <tr> <td><code>@BiocondaBot please add label</code></td> <td>Add the <code>please review & merge</code> label.</td> </tr> <tr> <td><code>@BiocondaBot please fetch artifacts</code></td> <td>Post links to CI-built packages/containers. <br />You can use this to test packages locally.</td> </tr> </table>

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mikecormier

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Devon Ryan

commit sha fa6902ed1f6ced82dd6e6e2d790641bc04cdd63c

Update meta.yaml

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Devon Ryan

commit sha 655b57a9dedf211209e9f146293f08b6666cab31

Bumps for pinning updates

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Devon Ryan

commit sha 714a98a478b65f59ff10355acbbb060cf855d464

oops, forgot the patch

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Devon Ryan

commit sha 22d0ef5fdd4d4f77d08e7eb6474ea4e3f552ccd4

revert debugging remnant

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pull request commentconda-forge/r-densityclust-feedstock

Fix a segfault

@conda-forge-admin please rerender

dpryan79

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PR opened conda-forge/r-densityclust-feedstock

Fix a segfault

I'll let this set here a bit to see if upstream accepts my PR fix in a timely manner. But since this CRAN package hasn't been updated in years I expect this is the only way to fix things in production.

Checklist

  • [x] Used a personal fork of the feedstock to propose changes
  • [x] Bumped the build number (if the version is unchanged)
  • [ ] Reset the build number to 0 (if the version changed)
  • [x] Re-rendered with the latest conda-smithy (Use the phrase <code>@<space/>conda-forge-admin, please rerender</code> in a comment in this PR for automated rerendering)
  • [x] Ensured the license file is being packaged.

<!-- Please note any issues this fixes using closing keywords: -->

<!-- Please add any other relevant info below: -->

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Devon Ryan

commit sha aad25a47d26c5401c50d2e3471c4e046d083de66

Bulk (#31502) * bulk update for bioconductor 3.14 * bulk update for bioconductor 3.14 (new packages) * fix omnipathr * rerun bulk * update bulk * bulk updates * bulk updates * bulk update * bulk update * bulk update * bulk update * bulk update * bulk update * bulk update * bulk updates * bulk update * bulk update * bulk update * bulk update * debug a data package * bulk update * bulk update * bulk updates * bulk update * bulk update * bulk update * bulk update * bulk update * bulk update * bulk update * bulk update * bulk update lumi * bulk update * bulk update * bulk update * bulk update * finish bulk * cleanup Co-authored-by: Devon Ryan <devon.ryan@genedata.com> Co-authored-by: Marcel Bargull <marcel.bargull@udo.edu>

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Bioconda Bot

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[ci skip] Merge PR 31499 Merge PR #31499, commits were: * Update rust-bio-tools to 0.30.2

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Ray

commit sha a7bdea1c1a2449255f980cba48d1402f56522bc3

[ci skip] Merge PR 31485 Merge PR #31485, commits were: * Update meta.yaml * Update meta.yaml * add virstrain recipes * add virstrain recipes * add virstrain recipes * add virstrain recipes * add virstrain recipes

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Douglas Lowe

commit sha 68c3da0af3017e7665b6c15c9282d055619cb2fb

[ci skip] Merge PR 31471 Merge PR #31471, commits were: * removing explicit schema-salad dep for toil * relax schema-salad versions for toil schema-salad is needed for cwltool - so we should let cwltool set the version needed (or we'll get build conflicts). * Bump build number * Toil CWL dependency updated to 3.1.20211020155521

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qdu-bioinfo

commit sha 11a0f02a9226c377c1cbaaef0d34f35779e76f37

[ci skip] Merge PR 31501 Merge PR #31501, commits were: * [fix]: remove useless arugments

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qibebt-bioinfo

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[ci skip] Merge PR 31503 Merge PR #31503, commits were: * [fix]: add make argument

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Bioconda Bot

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[ci skip] Merge PR 31507 Merge PR #31507, commits were: * Update atlas-gene-annotation-manipulation to 1.1.0

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Devon Ryan

commit sha 999da3422b487d79d7dafc0bfcce6e0ed60eb382

[ci skip] Merge PR 31504 Merge PR #31504, commits were: * requirements first * Remove some stuff from the blacklist

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zhenxian

commit sha 16b4dc33420993d56fef901421c05ab24b077bf9

update to version v0.1-r8 (#31509)

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Diogo Macedo

commit sha 9b5822d5027b0237b8ba3b5ef8f8c1f99098b40a

[coast] Update meta.yaml (#31511) * Update meta.yaml Forgot to update dependacies when the autobump happened * Update meta.yaml incremented the build nº

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Ray

commit sha 3c895c943065d324a4693216c13dfed54fdbfa62

[ci skip] Merge PR 31512 Merge PR #31512, commits were: * Merge branch 'master' into virstrain * add virstrain recipes

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Bioconda Bot

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Update perl-fastx-abi to 1.0.1 (#31514)

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Devon Ryan

commit sha 80201b00ce591cd86d88c127d276c848d4522b6d

[ci skip] Merge PR 31510 Merge PR #31510, commits were: * change packages * More blacklisted bioconductor packages

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Maxim Skoryk

commit sha c0bddb9a6af9488bc9a52a6e09bd32047c3e54ab

[ci skip] Merge PR 31506 Merge PR #31506, commits were: * Build against current R * Update maintainers * add recipe

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Devon Ryan

commit sha 3b500699b9f57598dcc7e3bfc7f2eac937d9ff4f

[ci skip] Merge PR 31523 Merge PR #31523, commits were: * OK, one at a time * Remove some bioconductor packages from the blacklist

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Bioconda Bot

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[ci skip] Merge PR 31525 Merge PR #31525, commits were: * Update vardict-java to 1.8.3

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Bioconda Bot

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Update mikado to 2.3.3 (#31529)

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Bioconda Bot

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Update mirtop to 0.4.24 (#31515)

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Devon Ryan

commit sha 1699e19190380e2e04944283ed9c69665151a81a

[ci skip] Merge PR 31528 Merge PR #31528, commits were: * try more * try other bioc packages

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Bioconda Bot

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[ci skip] Merge PR 29008 Merge PR #29008, commits were: * Update dependencies for coloc 5.1.0 https://github.com/chr1swallace/coloc/blob/v5.1.0/DESCRIPTION https://github.com/chr1swallace/coloc/blob/v3.1/DESCRIPTION * Update r-coloc to 5.1.0

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Devon Ryan

commit sha ac12569ad279bfc343c8cbb93ba774b01f397e52

Remove 3 recipes, closes #32419 (#32427) Co-authored-by: Devon Ryan <devon.ryan@genedata.com>

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issue closedbioconda/bioconda-recipes

Transfer recipes `seqlike`, `weblogo` and `python-codon-tables` to conda-forge

This is in continuation of the previous conversation with biononda-team member @dpryan79 for PR https://github.com/conda-forge/staged-recipes/pull/17283.

SUMMARY:

The three recipes (seqlike, weblogo, python-codon-tables) were managed by bioconda channel. Since the maintainers of seqlike wanted it on conda-forge, we started working on porting all three library-recipes from bioconda channel to conda-forge channel, with permission from bioconda-core-team. The other two libraries (weblogo, python-codon-tables) are dependencies of seqlike.

NOTE: Once the transfer happens, the bioconda recipes of the three packages will cease to exist.

See (here) and (here)

cc: @dpryan79 (from bioconda team)


:point_right: The approval from bioconda team: (comment)

Current Status

All three recipes have been created on conda-forge. Current maintainers have also been asked to let me know if they would like to be on the maintainers list. I am the maintainer of all three recipes. So, if anyone from bioconda channel wants to be a co-maintainer, please create an issue and ping me from the appropriate conda-forge feedstock.

TODO

Bioconda team: Please remove the recipes from bioconda channel to complete the transfer.

cc: @jaimergp (from conda-forge core team)

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sugatoray

PR merged bioconda/bioconda-recipes

Remove 3 recipes, closes #32419

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
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<details> <summary>Please use the following BiocondaBot commands:</summary>

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<table> <tr> <td><code>@BiocondaBot please update</code></td> <td>Merge the master branch into a PR.</td> </tr> <tr> <td><code>@BiocondaBot please add label</code></td> <td>Add the <code>please review & merge</code> label.</td> </tr> <tr> <td><code>@BiocondaBot please fetch artifacts</code></td> <td>Post links to CI-built packages/containers. <br />You can use this to test packages locally.</td> </tr> </table>

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dpryan79

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PR opened bioconda/bioconda-recipes

Remove 3 recipes, closes #32419

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

<details> <summary>Please use the following BiocondaBot commands:</summary>

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

<table> <tr> <td><code>@BiocondaBot please update</code></td> <td>Merge the master branch into a PR.</td> </tr> <tr> <td><code>@BiocondaBot please add label</code></td> <td>Add the <code>please review & merge</code> label.</td> </tr> <tr> <td><code>@BiocondaBot please fetch artifacts</code></td> <td>Post links to CI-built packages/containers. <br />You can use this to test packages locally.</td> </tr> </table>

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Agnieszka Danek

commit sha d58006748cd355e6b136004f816c93f5d9f367f6

Add agc (#32423) * agc * agc * agc * agc

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PR merged bioconda/bioconda-recipes

Add agc please review & merge

Adding recipe for AGC - Assembled Genomes Compressor (https://github.com/refresh-bio/agc). It is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
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agnieszkadanek

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pull request commentbioconda/bioconda-recipes

Add agc

Ah, yeah, that should suffice then.

agnieszkadanek

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PR opened thomasp85/densityClust

Fix numeric overflow

This closes #14 by fixing a potential numeric overflow during some integer arithmetic.

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Clustering by fast search and find of density peaks

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