NaegleLab/KSTAR issues and pull requests

#55 - Update configuration and resource files for v1.0 (major speedup by precomputed backgrounds)

Issue - State: open - Opened by knaegle 4 days ago

#54 - Interactive Visualization feature

Issue - State: open - Opened by knaegle 22 days ago - 2 comments

#53 - New feature of precomputed - finalizing the flexibility of behavior

Issue - State: open - Opened by knaegle about 2 months ago - 3 comments

#52 - "Could not convert string 'Y845' to numeric" error when using the "calculate.KinaseActivity()" function.

Issue - State: open - Opened by liuxiaoxian 5 months ago - 4 comments

#51 - Add example config file in the help documentation

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

#50 - Inspection: Would like to know what the evidence is that is related to a kinase activity

Issue - State: closed - Opened by knaegle about 2 years ago - 1 comment

#49 - Add Question submission and FAQ to KSTAR documents

Issue - State: closed - Opened by knaegle about 2 years ago

#48 - Visualization of evidence used in calculation

Issue - State: closed - Opened by knaegle about 2 years ago - 1 comment

#47 - Use of singularity requires pulling of docker image before running, but would be best if nextflow automatically did this

Issue - State: open - Opened by srcrowl about 2 years ago

#46 - Error when mapping with sites: 'PEPTIDE_ID' is not defined in experiment_mapper.py

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

#45 - Generate_random_experiments: 'Dataframe object has no attribute 'to_table'

Issue - State: closed - Opened by srcrowl almost 4 years ago

#44 - Bj8th

Pull Request - State: closed - Opened by bj8th about 4 years ago

#43 - Random activity not picking up the activity data columns

Issue - State: closed - Opened by knaegle about 4 years ago

#42 - Prune runs out of time, even on cluster -- save finished states and add gentle restart/continue

Issue - State: closed - Opened by knaegle about 4 years ago

#41 - Memory issues in random dataset generation and processing

Issue - State: open - Opened by knaegle about 4 years ago - 1 comment

#40 - Add False Positive Rate feature for activities and mann whitney

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#39 - added setup and prune run information

Pull Request - State: closed - Opened by bj8th about 4 years ago

#38 - Dotplot: Clustering not updating xtick labels and context

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#37 - Mw dev

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

#36 - Random dataset generation should allow study bias type and have warning threshold

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#35 - ST dataset generation failing, appears to select non-integer compendia

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#34 - kinase activities causing errors

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#33 - Bj8th dev

Pull Request - State: closed - Opened by bj8th about 4 years ago

#32 - issue with assembling from parallel processing large results

Issue - State: closed - Opened by knaegle about 4 years ago - 2 comments

#31 - data_columns is not overriding all data columns in activities analysis

Issue - State: closed - Opened by knaegle about 4 years ago

#30 - All multicore processing areas should take number of cores or proportion of cores

Issue - State: closed - Opened by knaegle about 4 years ago

#29 - Update status in activity log for random experiments

Issue - State: open - Opened by knaegle about 4 years ago

#28 - Plotting, allow legend naming

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#27 - Plotting - include separation of labels

Issue - State: closed - Opened by knaegle about 4 years ago

#26 - Uniquify mapping of compendia

Issue - State: open - Opened by knaegle about 4 years ago - 1 comment

#25 - Random dataset generation is creating incorrect number of evidences for experiments

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#24 - Normalization for threshold set as > vs. >=

Issue - State: closed - Opened by knaegle about 4 years ago

#23 - Random dataset generation does not encode for GREATER bool

Issue - State: closed - Opened by knaegle about 4 years ago

#22 - KSTAR normalization error in TCell example

Issue - State: closed - Opened by knaegle about 4 years ago

#21 - kinase activities should be in same order as experiment data frame

Issue - State: closed - Opened by knaegle about 4 years ago

#20 - kinase_activities has dropped experiment column

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#19 - Implement Mann Whitney U significance interpretation

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#18 - Implement Mann Whitney U Test as a method for pvalue

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#17 - Test network generation by applying to GPS/PhosphoPICK

Issue - State: closed - Opened by knaegle about 4 years ago

#16 - Create a stability_analysis class

Issue - State: open - Opened by knaegle about 4 years ago

#15 - Documentation of and for Network generation

Issue - State: closed - Opened by knaegle about 4 years ago

#14 - Since KinaseActivity requires mapping, why the need for evidence_columns?

Issue - State: closed - Opened by knaegle about 4 years ago

#13 - KinaseActivity object should store params, these should be used for random generation by default as part of class

Issue - State: closed - Opened by knaegle about 4 years ago - 2 comments

#12 - Phosphotype (pevent) should filter the experiments based on substrate type

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#11 - Document how aggregate handles 'mean' when one peptide or more has NaN

Issue - State: closed - Opened by knaegle about 4 years ago

#10 - Mapping should handle isoform accessions

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#9 - Use GLOBALS in kstar.config

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#8 - Finish Installation instructions

Issue - State: closed - Opened by knaegle about 4 years ago

#7 - Fix project so import names are short and make sense

Issue - State: closed - Opened by knaegle about 4 years ago

#6 - Document use of run_kstar.py on real example

Issue - State: closed - Opened by knaegle about 4 years ago - 2 comments

#5 - Fix docstring sphinx errors

Issue - State: closed - Opened by knaegle about 4 years ago

#4 - run_kstar.py --odir required, but not stated

Issue - State: closed - Opened by knaegle about 4 years ago

#3 - Update mapper to use data:<type>:<name>

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#2 - run_kstar flag is unlegible

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

#1 - run_kstar should allow for SITE or PEPTIDE

Issue - State: closed - Opened by knaegle about 4 years ago - 1 comment

GitHub / NaegleLab/KSTAR issues and pull requests