shuzhao-li/asari issues and pull requests

#76 - Need to modify 'number_of_samples' in project.json if enable --drop_unaligned_samples

Issue - State: closed - Opened by YuanyeChi about 1 year ago - 2 comments

#75 - -o '.' results in hidden output directory on MacOS/Linux

Issue - State: closed - Opened by jmmitc06 about 1 year ago - 1 comment
Labels: bug

#74 - Default Params from Other Instruments

Issue - State: open - Opened by jmmitc06 about 1 year ago
Labels: enhancement

#73 - Pickle Alternative

Issue - State: open - Opened by jmmitc06 about 1 year ago
Labels: enhancement

#72 - Autoheight (other params) must be global for experiments that will be joined

Issue - State: closed - Opened by jmmitc06 about 1 year ago - 1 comment

#71 - Parallelize Mass Grid Construction

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#70 - Parallelize RT Alignment

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#69 - Minimize external depencies

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#68 - Better Testing

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement, help wanted

#67 - Mass Tracks Should be Sparse

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#66 - Meta Experiment Trackability

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#65 - Caching of Pickles

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#64 - Unified Methods for Experiments and MetaExperiments

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#63 - Auto-optimize params for asari

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#62 - Autoheight for retention time alignment anchors

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#61 - non-relative mz error

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#60 - Add Readme to Results

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#59 - mzXML support and other file formats

Issue - State: open - Opened by jmmitc06 over 1 year ago - 1 comment
Labels: enhancement

#58 - How to pick reference sample for alignment ?

Issue - State: closed - Opened by amnahsiddiqa over 1 year ago - 5 comments
Labels: enhancement

#57 - Implement Join Function/Workflow

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 4 comments

#56 - Autodetect ionization mode from mzML

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#55 - Output m/z and rt values of ions used for alignment

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#54 - interpolated ref RT producing infinity

Issue - State: closed - Opened by shuzhao-li over 1 year ago - 3 comments

#53 - Support chained experiments linked by common samples

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 3 comments

#52 - Asari viz is broken

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#51 - Import statements are too broad

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment

#50 - Asari has no functions / modules when interfacing thru reticulate

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 4 comments

#49 - Retention Time Alignment Poorly Regularized Under Some Conditions

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 4 comments
Labels: bug

#48 - Asari Viz, toggle to show all features vs. preferred features

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: enhancement

#47 - Asari Viz Should Report Parameters Used for Analysis

Issue - State: open - Opened by jmmitc06 over 1 year ago - 1 comment
Labels: enhancement

#46 - Remove Prominence Window from Parameters.yaml

Issue - State: closed - Opened by jmmitc06 over 1 year ago

#45 - Missing peaks

Issue - State: closed - Opened by xulei99 over 1 year ago - 17 comments

#44 - Alignment warning

Issue - State: closed - Opened by xulei99 over 1 year ago - 2 comments

#43 - Data with memory issue

Issue - State: closed - Opened by xulei99 over 1 year ago - 4 comments

#42 - Sample Blacklist for RT Reference

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 1 comment
Labels: enhancement

#41 - Improve build_chromatogram_by_mz_clustering in m/z dense regions

Issue - State: open - Opened by jmmitc06 over 1 year ago
Labels: bug, enhancement

#40 - Can asari distinguish the number of charges?

Issue - State: closed - Opened by xieyying over 1 year ago - 7 comments

#39 - Processing Nano-LC Data Very Slow

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 4 comments

#38 - small change on developers guide

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

#37 - Merge after integrated with readthedocs

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

#36 - Reference sample selection could be made more robust

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 4 comments

#35 - To update annotation to be more consistent with metDataModel

Issue - State: open - Opened by shuzhao-li over 1 year ago
Labels: enhancement

#34 - facing error using asari dashboard

Issue - State: closed - Opened by amnahsiddiqa over 1 year ago - 1 comment

#33 - Target extract seems to return only the first match in full feature table?

Issue - State: closed - Opened by gmhhope over 1 year ago - 5 comments

#32 - Error with `np.str` present in kiupu pkg due to version upgrade of numpy (> 1.24)

Issue - State: closed - Opened by gmhhope almost 2 years ago

#31 - suppress khipu warnings

Issue - State: closed - Opened by shuzhao-li almost 2 years ago - 1 comment

#30 - Remove __hacked_lowess__ in future version

Issue - State: closed - Opened by shuzhao-li almost 2 years ago - 1 comment

#29 - To improve SNR calculation to a curve fitting

Issue - State: closed - Opened by shuzhao-li almost 2 years ago - 1 comment

#28 - Asari skip all later samples with mzML processing error

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

#27 - Error when using docker-converted singularity container

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

#26 - Include export of peak list in concise format - to use for 2ndary annotation

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

#25 - Throttle of viz loading

Issue - State: open - Opened by shuzhao-li about 2 years ago
Labels: enhancement

#24 - default to removing pickle folder after processing

Issue - State: closed - Opened by shuzhao-li over 2 years ago

#23 - Include version number in project.json

Issue - State: closed - Opened by shuzhao-li over 2 years ago

#22 - Alternative way to run Asari using docker-compose

Issue - State: closed - Opened by gmhhope over 2 years ago

#21 - Docker limitation of resource handicap running Asari in docker

Issue - State: closed - Opened by gmhhope over 2 years ago

#20 - Errorred running docker pull shuzhao/asari

Issue - State: closed - Opened by amnahsiddiqa over 2 years ago - 6 comments

#19 - scipy find_peaks misses some peaks with high baseline noise

Issue - State: closed - Opened by shuzhao-li over 2 years ago - 1 comment

#18 - Some features/peaks are not in annotation output due to bug in JMS

Issue - State: closed - Opened by shuzhao-li over 2 years ago - 1 comment

#17 - help flag asari ; not found via home brewed python3 interpreter installation

Issue - State: closed - Opened by amnahsiddiqa over 2 years ago - 1 comment

#16 - narrower RT window for empCpd construction

Issue - State: open - Opened by shuzhao-li over 2 years ago
Labels: enhancement

#15 - Bug in mass track centroid assembly

Issue - State: closed - Opened by shuzhao-li over 2 years ago - 1 comment

#14 - Add QC subcommand and reporting

Issue - State: open - Opened by shuzhao-li over 2 years ago - 1 comment
Labels: enhancement

#13 - Add versions into project.json

Issue - State: closed - Opened by shuzhao-li over 2 years ago

#12 - Add targeted extraction

Issue - State: closed - Opened by shuzhao-li over 2 years ago - 1 comment

#11 - option to designate reference sample

Issue - State: closed - Opened by shuzhao-li over 2 years ago - 1 comment

#10 - memory issues while using -- autoheight TRUE;

Issue - State: closed - Opened by amnahsiddiqa over 2 years ago

GitHub / shuzhao-li/asari issues and pull requests