genomicsengland/gel-coverage issues and pull requests

#67 - Bump ujson from 1.35 to 5.4.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, python

#66 - Bump numpy from 1.11.2 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, python

#65 - Bump numpy from 1.11.2 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#64 - Bump ujson from 1.35 to 5.2.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#63 - Bcb 219 force int confidence comparison

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

#62 - Update setup.py

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

#61 - Update setup.py

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

#60 - BCB-215 new PanelApp endpoint and confidence

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

#59 - IS-452/confidence filter

Pull Request - State: closed - Opened by Antonior26 about 4 years ago

#58 - IS-263

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

#57 - hotfix/1.4.x: implemented re-try to deal with CellBase silent issue i…

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

#56 - Fix setup script

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

#55 - Fix something

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

#54 - Remove unwanted references to gel.zone

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

#53 - remove some .gel.zone things

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

#52 - Release 1.4.2 and open sourcing

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

#51 - improve setup

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

#50 - Feature/mock coverage data

Pull Request - State: open - Opened by priesgo over 6 years ago

#49 - add option --exon-padding

Pull Request - State: closed - Opened by priesgo almost 7 years ago

#48 - Hotfix/bed generation

Pull Request - State: closed - Opened by priesgo almost 7 years ago

#47 - Hotfix/bed generation

Pull Request - State: closed - Opened by priesgo almost 7 years ago

#46 - Release v1.4.0

Pull Request - State: closed - Opened by priesgo almost 7 years ago

#45 - Added assembly parameter to PanelApp queries

Pull Request - State: closed - Opened by Antonior26 almost 7 years ago - 1 comment

#44 - Version 1.3.1

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

#43 - Release gel-coverage 1.3.0

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

#42 - Feature bertha 303

Pull Request - State: closed - Opened by priesgo about 7 years ago - 2 comments

#41 - Bertha 303 replace genomic coordinates from cellbase to file

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

#40 - #BERTHA-303: Replace genomic coordinates from Cellbase to file

Pull Request - State: closed - Opened by enricserra about 7 years ago - 1 comment

#39 - Bertha 303 replace genomic coordinates from cellbase to file

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

#38 - Bertha 303 replace genomic coordinates from cellbase to file

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

#37 - Updating develop with master

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

#36 - BERTHA-239

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

#35 - v1.2.2

Pull Request - State: closed - Opened by priesgo over 7 years ago - 1 comment

#34 - SystemError: Input gene list is not correct

Issue - State: open - Opened by enricserra over 7 years ago - 3 comments

#33 - Error when all transcripts are filtered out

Issue - State: closed - Opened by priesgo over 7 years ago - 1 comment

#32 - Calculate standard deviation at several genomic levels

Issue - State: closed - Opened by priesgo over 7 years ago - 1 comment

#31 - Updating setup.py

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

#30 - Segmentation fault for GRCh38 coverage analysis

Issue - State: closed - Opened by priesgo almost 8 years ago - 5 comments

#29 - Uneveness of coverage metric is not being weighted and the result might be biased

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

#28 - fixing package definition in setup.py

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

#27 - Develop

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

#26 - fixed bug in

Pull Request - State: closed - Opened by Antonior26 almost 8 years ago

#25 - Dev

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

#24 - remove bam2wig, add flag to avoid running coding region analysis, upd…

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

#23 - Dev

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

#22 - support for multiple panels

Issue - State: open - Opened by Antonior26 almost 8 years ago - 2 comments

#21 - Add support for chromosome chr prefix on cellbase helper

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#20 - Coverage pipeline usage of different chromosome identifiers conventions

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#19 - Add statistics at chromosome level for whole genome and exome regions

Issue - State: closed - Opened by priesgo almost 8 years ago - 2 comments

#18 - Support NonN regions bed file for the whole genome coverage analysis

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#17 - Report not sequenced regions

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#16 - Add whole genome metric of coverage uneveness

Issue - State: closed - Opened by priesgo almost 8 years ago

#15 - Add GRCh38 support to wrapper script

Issue - State: closed - Opened by katherinesmith almost 8 years ago - 6 comments

#14 - Stress test: run the analysis on a whole genome file

Issue - State: closed - Opened by priesgo almost 8 years ago - 2 comments

#13 - Automate test data download by making it available in OpenCGA

Issue - State: open - Opened by priesgo almost 8 years ago

#12 - Parametrize the configuration file

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#11 - Compute coverage statistics at panel level

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#10 - Compute coverage statistics at gene level using the union transcript

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#9 - Include a parametrizable number of bases up and downstream of each exon

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#8 - Requirements meeting

Issue - State: closed - Opened by cboustred almost 8 years ago - 9 comments

#7 - Cache reference genome BED obtained from CellBase

Issue - State: open - Opened by priesgo almost 8 years ago

#6 - Parametrize the exclusion of genes from the input panel/s based on confidence

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#5 - Parametrize analysis region by: transcript list

Issue - State: open - Opened by priesgo almost 8 years ago

#4 - Parametrize analysis region by: panels, gene list or whole exome

Issue - State: closed - Opened by priesgo almost 8 years ago - 1 comment

#3 - Support configuration file and create one example configuration file

Issue - State: closed - Opened by priesgo almost 8 years ago - 5 comments

#2 - Filter transcripts to be used by basic flag (GeneCode genes) and also biotype

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

#1 - Format output in computer-friendly format

Issue - State: closed - Opened by priesgo almost 8 years ago - 2 comments

GitHub / genomicsengland/gel-coverage issues and pull requests