Jhsmit/PyHDX

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Derive ΔG for single residues from HDX-MS data

Stars: 32
Forks: 14
Open beginner issues: 0
Indexed issues: 56

Dominant language: Jupyter Notebook
License: MIT
Last GitHub push: Dec 17, 2025
Latest indexed: Sep 18, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue
PR merge metrics: No merged PRs in 30d

Open All

56 issues indexed so far

use curve peeling/stripping for initial guesses of exponential fit Open

enhancement

Jhsmit/PyHDX#29 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
check edge cases for ignoring prolines Open

bug invalid

Jhsmit/PyHDX#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
download txt file with data summary Open

enhancement

Jhsmit/PyHDX#41 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
view vertical line in both plots during mouseover event Open

enhancement

Jhsmit/PyHDX#57 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
allow export of k_int Open

enhancement GUI

Jhsmit/PyHDX#70 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
k_int vs kint Open

good first issue

Jhsmit/PyHDX#81 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
figure panels need dynamic titles Open

GUI

Jhsmit/PyHDX#98 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
pytorch diff eqns Open

Jhsmit/PyHDX#130 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Correct k_int for percentage D Open

enhancement investigate

Jhsmit/PyHDX#136 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Add deltaG graph to link x range Open

enhancement GUI

Jhsmit/PyHDX#155 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Streched exponential fitting Open

enhancement wontfix

Jhsmit/PyHDX#159 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Allow NaN in batch fitting Open

enhancement Fitting investigate

Jhsmit/PyHDX#174 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Exported dataframes with r_numbers should have sequence information in them Open

enhancement

Jhsmit/PyHDX#193 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Relay error messages to log in GUI Open

enhancement GUI

Jhsmit/PyHDX#194 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Log dir in config Open

enhancement GUI

Jhsmit/PyHDX#196 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
color transform as yaml Open

enhancement GUI

Jhsmit/PyHDX#202 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
C terminal residue intrinsic rate of exchange Open

investigate

Jhsmit/PyHDX#211 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
docs fitting example math render Open

documentation

Jhsmit/PyHDX#224 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Reloading fit results is slow Open

enhancement Fitting

Jhsmit/PyHDX#229 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Allow gracious failing of estimating errors Open

enhancement Fitting good first issue

Jhsmit/PyHDX#230 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Initial guesses are slow Open

discussion enhancement Fitting investigate

Jhsmit/PyHDX#233 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Plot output should take alignments Open

enhancement

Jhsmit/PyHDX#235 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
fit result output include standard deviation of mse loss Open

enhancement Fitting

Jhsmit/PyHDX#236 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Force ddG color transform color maps to be divergent by default Open

enhancement good first issue GUI

Jhsmit/PyHDX#238 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Glasbey default colors when using discrete Open

enhancement good first issue GUI

Jhsmit/PyHDX#240 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Export session button needs loading indicator Open

enhancement good first issue GUI

Jhsmit/PyHDX#241 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Fit iterations per second in log output Open

enhancement GUI

Jhsmit/PyHDX#245 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Dask client should be optional Open

enhancement GUI

Jhsmit/PyHDX#261 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Allow other data formats as input Open

enhancement

Jhsmit/PyHDX#262 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Pyhdx process cli interface Open

enhancement

Jhsmit/PyHDX#263 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Unify hdx_set and hdxm_set Open

Jhsmit/PyHDX#265 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Unify fit_result fitresult Open

enhancement

Jhsmit/PyHDX#266 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Documentation for `pyhdx process` Open

enhancement

Jhsmit/PyHDX#268 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Test pickling / weighted averge initial guesses Open

enhancement Fitting

Jhsmit/PyHDX#270 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Align dataframes function should take dicts only Open

Jhsmit/PyHDX#274 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Web application reference docs superclass info not useful Open

documentation

Jhsmit/PyHDX#275 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Proplot pinned requirement Open

enhancement

Jhsmit/PyHDX#276 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
state spec yamls do not support relative paths when using the GUI Open

bug GUI

Jhsmit/PyHDX#277 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Peptide view needs a hover tool Open

enhancement good first issue GUI

Jhsmit/PyHDX#280 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Feature request: export ΔRFU linear bars grouped by state Open

enhancement GUI

Jhsmit/PyHDX#283 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Catch errors when inputting an invalid file in web app Open

bug GUI

Jhsmit/PyHDX#284 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Downsample exported loss in session files Open

enhancement GUI

Jhsmit/PyHDX#287 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
pdb files per protein state; include pdb files in exported session files Open

enhancement GUI

Jhsmit/PyHDX#288 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Setting values on a copy of dataframe Open

Jhsmit/PyHDX#298 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Residue offset in web application Open

enhancement GUI

Jhsmit/PyHDX#299 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Intersection of peptides between HDX measurements Open

enhancement GUI

Jhsmit/PyHDX#300 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Refresh c_term n_term defaults when switching experiment state Open

Jhsmit/PyHDX#304 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 18, 2026
Goodness of fit qualifiers feedback D-uptake fit Open

enhancement

Jhsmit/PyHDX#306 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Fitting with peptide weights Open

enhancement

Jhsmit/PyHDX#307 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
FutureWarning: pandas indexing Open

bug

Jhsmit/PyHDX#308 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026

Jhsmit/PyHDX

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