Ecosyste.ms: Issues

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

GitHub / sanger-pathogens/Bio-Tradis issues and pull requests

#132 - how is the insertion index calculated?

Issue - State: open - Opened by mpapange about 1 year ago - 6 comments

#131 - EdgeR not working with new R version?

Issue - State: open - Opened by iawarner about 1 year ago

#130 - Issues on running BioTraDIS on multiple contigs

Issue - State: open - Opened by Madhuskey1993 over 1 year ago - 1 comment

#129 - Essentiality function not working

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

#128 - Unable to install biotradis

Issue - State: open - Opened by voonkit over 2 years ago

#127 - -mm paramater not working as expected

Issue - State: open - Opened by martinclott about 3 years ago - 1 comment

#126 - Update README.md

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

#125 - tradis_comparison issue

Issue - State: open - Opened by pmireland over 3 years ago - 3 comments

#123 - Problem with insertion plots (files longer than they should be)

Issue - State: open - Opened by irilenia almost 4 years ago - 9 comments

#122 - need to update read end for soft-clipping as well

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

#121 - fixed bug in handling soft clipping at read start, updated tutorial

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

#120 - Possible issue with calculation of read start and ends in module Cigar.pm

Issue - State: closed - Opened by irilenia almost 4 years ago - 2 comments

#118 - add locales to Dockerfile

Pull Request - State: closed - Opened by puethe over 4 years ago

#117 - Essentiality analysis code

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

#116 - test failures with samtools v1.10

Issue - State: open - Opened by mr-c over 4 years ago - 1 comment

#115 - Update README.md

Pull Request - State: closed - Opened by thanhleviet over 4 years ago

#114 - Remove hardcoded path

Pull Request - State: closed - Opened by thanhleviet over 4 years ago

#113 - Update bacteria_tradis

Pull Request - State: closed - Opened by thanhleviet over 4 years ago

#111 - Removed '--force' for [@Starter]

Pull Request - State: closed - Opened by telatin about 5 years ago

#110 - installing biotradis on MacOS

Issue - State: closed - Opened by angelovangel about 5 years ago - 4 comments

#109 - Update TravisCI tests using Docker

Pull Request - State: closed - Opened by telatin about 5 years ago - 1 comment

#108 - Fixed relative path to ./lib problem in binaries using FindBin

Pull Request - State: closed - Opened by telatin about 5 years ago

#107 - Add relative path to ./lib via FindBin

Pull Request - State: closed - Opened by telatin about 5 years ago

#106 - Add relative path to ./lib via FindBin

Pull Request - State: closed - Opened by telatin about 5 years ago

#105 - Add relative path to lib/ via FindBin

Pull Request - State: closed - Opened by telatin about 5 years ago

#104 - Add relative path to ./lib via FindBin

Pull Request - State: closed - Opened by telatin about 5 years ago

#103 - Add relative path to ./lib via FindBin

Pull Request - State: closed - Opened by telatin about 5 years ago

#102 - Fix missing library

Pull Request - State: closed - Opened by telatin about 5 years ago

#101 - Add conda badge to README

Pull Request - State: closed - Opened by ssjunnebo over 5 years ago

#100 - How to deal with biological replicates - tradis_essentiality.R

Issue - State: closed - Opened by subwaystation over 5 years ago - 4 comments

#99 - Update README.md

Pull Request - State: closed - Opened by thanhleviet over 5 years ago

#98 - Added changelog

Pull Request - State: closed - Opened by ssjunnebo over 5 years ago

#97 - Include tests in README

Pull Request - State: closed - Opened by ssjunnebo over 5 years ago

#96 - update version for cpan

Pull Request - State: closed - Opened by ssjunnebo almost 6 years ago

#95 - Add to codecov

Pull Request - State: closed - Opened by ssjunnebo almost 6 years ago

#94 - Change TryCatch to Try::Tiny

Pull Request - State: closed - Opened by ssjunnebo almost 6 years ago

#93 - fix typo in badge

Pull Request - State: closed - Opened by ssjunnebo almost 6 years ago

#92 - Include TOC

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#91 - 621538 docker

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#90 - 621538 docker

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#89 - include reference genome for cram

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#88 - Revert "Replace cram file without reads"

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#87 - Replace cram file without reads

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#86 - Using Bio-Tradis to analyze mariner-transposon library

Issue - State: closed - Opened by minisciencegirl over 6 years ago - 8 comments

#85 - update tutorial for ENA switch to https (from http)

Pull Request - State: closed - Opened by lbarquist over 6 years ago

#84 - Installation on Ubuntu 17.10 fails

Issue - State: closed - Opened by apeltzer over 6 years ago - 2 comments
Labels: installation

#83 - Port 18 volume discrepancy?

Issue - State: closed - Opened by ucpete over 6 years ago - 6 comments

#82 - include last base of annotation in insertion count

Pull Request - State: closed - Opened by lbarquist over 6 years ago

#81 - Duplicate genes

Issue - State: closed - Opened by ppgardne over 6 years ago - 4 comments

#80 - Installing Bio-Tradis Fail

Issue - State: closed - Opened by minisciencegirl over 6 years ago - 6 comments

#79 - Rename license file'

Pull Request - State: closed - Opened by ssjunnebo about 7 years ago

#78 - update AUTHORS and rename LICENSE

Pull Request - State: closed - Opened by ssjunnebo about 7 years ago

#77 - Tmp file time stamp

Pull Request - State: closed - Opened by ssjunnebo about 7 years ago

#76 - try localtime for tmp file timestamp

Pull Request - State: closed - Opened by ssjunnebo about 7 years ago

#75 - cpan update?

Issue - State: closed - Opened by lbarquist about 7 years ago - 1 comment

#74 - modified ranges to accommodate higher density insertion data

Pull Request - State: closed - Opened by lbarquist over 7 years ago

#73 - removed File::Slurp

Pull Request - State: closed - Opened by vaofford over 7 years ago

#72 - dont add POD to R scripts

Pull Request - State: closed - Opened by andrewjpage almost 8 years ago

#71 - tradis_comparison.R error

Issue - State: closed - Opened by DanMediati almost 8 years ago - 3 comments

#70 - change to dist zilla starter bundle

Pull Request - State: closed - Opened by nds almost 8 years ago

#69 - switch PCR primers

Pull Request - State: closed - Opened by andrewjpage about 8 years ago

#68 - updated readme

Pull Request - State: closed - Opened by lbarquist about 8 years ago

#65 - Merge Roys changes

Pull Request - State: closed - Opened by andrewjpage about 8 years ago

#64 - Added support for samtools 1.x, -n multi-core option and fixed -m default

Pull Request - State: closed - Opened by RoyChaudhuri about 8 years ago - 2 comments
Labels: bug, enhancement

#63 - Error in step 3.5 of bacteria_tradis, using samtools 1.3

Issue - State: closed - Opened by juanu about 8 years ago - 1 comment

#62 - added recipes (again)

Pull Request - State: closed - Opened by lbarquist over 8 years ago

#61 - fixes for revision

Pull Request - State: closed - Opened by lbarquist over 8 years ago

#60 - bugfix to tradis_essentiality.R

Pull Request - State: closed - Opened by lbarquist over 8 years ago

#59 - Bump the version number

Pull Request - State: closed - Opened by bewt85 over 8 years ago

#58 - Ticket 463867: What if a tag isn't found?

Pull Request - State: closed - Opened by bewt85 over 8 years ago

#57 - updated bacteria_tradis help messages

Pull Request - State: closed - Opened by lbarquist almost 9 years ago

#56 - Add package version module to dist zilla

Pull Request - State: closed - Opened by andrewjpage almost 9 years ago

#55 - Added sequencing recipes

Pull Request - State: closed - Opened by lbarquist almost 9 years ago

#54 - updated help messages for R scripts

Pull Request - State: closed - Opened by lbarquist almost 9 years ago

#53 - POD formatting

Pull Request - State: closed - Opened by andrewjpage almost 9 years ago

#52 - Simplify installation

Pull Request - State: closed - Opened by andrewjpage almost 9 years ago

#51 - Ticket 473325: Install two different versions of SAMTOOLS

Pull Request - State: closed - Opened by bewt85 almost 9 years ago

#50 - Add TravisCI support

Pull Request - State: closed - Opened by bewt85 about 9 years ago - 1 comment

#49 - fixed filtering bug

Pull Request - State: closed - Opened by lbarquist about 9 years ago

#48 - Updated shebang line in R scripts for portability

Pull Request - State: closed - Opened by carlacummins about 9 years ago

#47 - added installation notes

Pull Request - State: closed - Opened by lbarquist about 9 years ago

#46 - only require 2 command line args, not 3

Pull Request - State: closed - Opened by lbarquist over 9 years ago

#45 - Bug fixes and added features

Pull Request - State: closed - Opened by carlacummins over 9 years ago

#44 - Adding tabix a prerequisite

Pull Request - State: closed - Opened by js21 over 9 years ago

#43 - Cram file output

Pull Request - State: closed - Opened by andrewjpage over 9 years ago

#42 - Code is now cross-platform

Pull Request - State: closed - Opened by js21 over 9 years ago

#41 - Pass through samtools exec and verbose mode

Pull Request - State: closed - Opened by andrewjpage over 9 years ago

#40 - Cram support

Pull Request - State: closed - Opened by andrewjpage over 9 years ago

#39 - added the missing test files

Pull Request - State: closed - Opened by js21 over 9 years ago

#38 - suppressed uninitialised warnings when importing PE data

Pull Request - State: closed - Opened by carlacummins over 9 years ago

#37 - Tabix indexed plot files in place

Pull Request - State: closed - Opened by js21 over 9 years ago

#35 - fixed typo

Pull Request - State: closed - Opened by lbarquist over 9 years ago

#34 - feature addition to tradis_comparison, bugfix tradis_essentiality

Pull Request - State: closed - Opened by lbarquist over 9 years ago

#33 - Added AUTHORS file

Pull Request - State: closed - Opened by aslett1 almost 10 years ago