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42b428e
Create .gitignore
Congm12 May 6, 2022
86a8365
Merge branch 'master' into main
Congm12 May 6, 2022
e4799e6
add HMM with NB and BetaBinom emission probabilities and site-specifi…
Congm12 May 18, 2022
ce49d30
Changed log v to per chromosome
MayaGupta27 Jun 7, 2022
a8c2c63
Minor change to backward algorithm
MayaGupta27 Jun 7, 2022
3f86daa
fix params initialization in Weighted_BetaBinomMixture to avoid out o…
Congm12 Jun 8, 2022
59617a1
fix bug in hmm_NB_sharedstates (based on hmmlearn) for multiple seque…
Congm12 Jun 8, 2022
40060c0
simplify the forward/backward lattice code to use kronecker product; …
Congm12 Jun 8, 2022
b4689e8
Merge branch 'main' of https://github.com/raphael-group/locality-clus…
Congm12 Jun 8, 2022
bdb8d84
add user defined initialization for NB and BetaBinom mean; to reduce …
Congm12 Jun 10, 2022
583c647
adjust the M step convergence criteria; add a heuristic to speed up M…
Congm12 Jun 17, 2022
5ea619b
multi-sample + allow fixing parameters
Congm12 Jul 15, 2022
32fbfb8
fix a variable naming bug
Congm12 Jul 15, 2022
0304e09
add phase switch utility functions
Congm12 Jul 21, 2022
a0621ed
update default parameters in pipeline_baum_welch; shrink input size b…
Congm12 Jul 21, 2022
ddfc6cf
address the 0 issue in RDR signal; update the initialization in pipel…
Congm12 Sep 28, 2022
2167cda
add initialize HMM RDR in log/original space option; add gurobi for f…
Congm12 Oct 6, 2022
141c246
a trick to speed up M step
Congm12 Oct 13, 2022
db6ef79
adding a scaling factor of genetic distance in computing phase switch…
Congm12 Oct 18, 2022
1087032
adding rdr-related scale factor for each clone to account for genome …
Congm12 Oct 18, 2022
caeee7f
trying making hmrf an easy-to-run script
Congm12 Oct 18, 2022
6b8aaa5
revert hmm_NB_BB_phaseswitch temporarily for git pull
Congm12 Oct 18, 2022
f8c748a
add back hmm code with scalefactor; fix the directory naming issue in…
Congm12 Oct 19, 2022
6e3de6f
add an example data for running HMM
Congm12 Oct 23, 2022
873e2f1
gaussian HMM + phase switch for hatchet2
Congm12 Oct 27, 2022
e35c902
update utility functions
Congm12 Nov 29, 2022
b067685
a full pipeline for BAF-only clones followed by using both RDR and BA…
Congm12 Jan 22, 2023
af6053f
filter DE genes, better integer copy number inference; leads to norma…
Congm12 Feb 9, 2023
5ef8887
Fixed minor error in initialization_by_gmm method
MayaGupta27 Apr 10, 2023
2148326
first phase and bin, and then run HMM without phase switch (variable …
Congm12 Apr 11, 2023
8d5c176
update to the latest hmm phase switch code
Congm12 Apr 11, 2023
8253d9f
Merge branch 'main' of https://github.com/raphael-group/locality-clus…
Congm12 Apr 11, 2023
1f8f962
parse input and output tables according to google-doc specification
Congm12 Jun 23, 2023
0953204
add a check for nan tumor purity
Congm12 Jun 23, 2023
b55c360
add an updated version of tumor UMI proportion in the mixture model; …
Congm12 Jun 23, 2023
9bf0c3b
clean up hmrf utility
Congm12 Jun 23, 2023
d2c1af9
add reordering between tissue position list, adata, and cellsnp-lite;…
Congm12 Jun 23, 2023
2fdaba4
change when to draw arrows for mirrored events
Congm12 Jun 23, 2023
db4616d
make the number of clones inferred using both BAF+RDR as a parameter
Congm12 Jun 23, 2023
5f17d24
change integer copy number inference to squared distances; add pipeli…
Congm12 Jun 23, 2023
b6aedc3
add supervised clone version; fix related bugs
Congm12 Jun 26, 2023
21fea42
add adjacency matrix construction using KNN and data parsing for slid…
Congm12 Jun 26, 2023
4b1f55c
remove an unused import dependency
Congm12 Jun 28, 2023
c50c006
update the supervised run as making pseudospot + run entire inference
Congm12 Jun 28, 2023
b025aa3
update supervised calicost and add min UMI threshold filtering in clo…
Congm12 Jul 4, 2023
4013bc8
update argparsing for joint samples
Congm12 Jul 4, 2023
92edd0e
fix the error in merging spots by min_spots or min_umis; change the f…
Congm12 Jul 4, 2023
c68937c
splitting clone spatial plot for supervised version into samples
Congm12 Jul 5, 2023
78dbdd9
addressing the NAN error when spaceranger outputs of different slices…
Congm12 Jul 6, 2023
79bd32e
add hatchet plotting and evaluation accuracy utility; fix bug related…
Congm12 Jul 11, 2023
c677109
update the variable for thresholding minimum SNP-covering umi per bin…
Congm12 Jul 16, 2023
d585720
add function to summarize to events
Congm12 Jul 16, 2023
65e1d84
update converting acn to state function in evaluation
Congm12 Jul 16, 2023
b65a85e
update post-thresholding of key events and highlighting in plots
Congm12 Jul 17, 2023
dc0a880
add plotting in joint, fix n_clone_rdr bug in processing
Congm12 Jul 26, 2023
8428c01
fix ties in merge clones by min_spots
Congm12 Jul 26, 2023
524399e
fix an edge case of merging bins across chrs
Congm12 Jul 31, 2023
569e256
add transition probability parameter for phasing
Congm12 Aug 3, 2023
d3ee6cf
add HMM transition for phasing in the input parsing step
Congm12 Aug 3, 2023
56f1c6d
update the integer copy number searching without ploidy constraint to…
Congm12 Aug 10, 2023
b8610e6
force at least 100 normal spots are used to remove bins potentially w…
Congm12 Aug 13, 2023
73a20e7
test fixing mean and betabinom dispersion in the test for bin-removal…
Congm12 Aug 13, 2023
9e7868d
add shared arg parse
Congm12 Aug 15, 2023
10b524b
fixing a bug introduced in the previous version for log phase transit…
Congm12 Aug 15, 2023
70ffdd6
removing testing for ploidy
Congm12 Aug 15, 2023
ef8f35c
import ploting utilities; multiple random initialization for initial …
Congm12 Aug 16, 2023
e064ecc
add integer copy number approach by scale factor from diploid state; …
Congm12 Aug 20, 2023
f33bdff
fix bug in arg parse and plotting functions
Congm12 Aug 27, 2023
e245a30
add accuracy evaluation for numbat, infercnv, and starch in utils
Congm12 Aug 27, 2023
f88af1b
more aggresive filter DE genes; enforce the same genomic bins to have…
Congm12 Aug 27, 2023
e7dc0b3
fix the error in merge pseudobulk about format of tumor proportion; u…
Congm12 Oct 9, 2023
f67f2a3
fix errors in edges cases; add more plotting functions
Congm12 Oct 11, 2023
46427e9
plotting 1d2d plots from dataframes
Congm12 Oct 12, 2023
9ffb83b
distribute transcript count of each gene to the overlapping bins prop…
Congm12 Oct 18, 2023
a9afa37
constrain to gene boundaries for blocking and binning
Congm12 Oct 21, 2023
dcfe7d9
fix bug in parse input; change the plotting of mirrored events to tri…
Congm12 Oct 21, 2023
cdd5c65
enable clone proportion info in plotting
Congm12 Oct 21, 2023
8802fba
fix bug in greedy binning; remove unused arguments in arg parse
Congm12 Oct 23, 2023
19cc0f6
change the schematic of mirrored event to triangles
Congm12 Oct 24, 2023
938b7ac
add purity threshold option in evaluation using hatchet functions
Congm12 Oct 24, 2023
ffd861c
wes comparison: add precision and recall of predicting aberrations bins
Congm12 Oct 25, 2023
0fde835
update expand_cnv function
Congm12 Oct 25, 2023
5331d32
remove nan of the input data frame in plotting function
Congm12 Oct 26, 2023
7db5f74
include more integer to state conversions in plot_hatchet
Congm12 Oct 28, 2023
54f46dd
update utils to convert variable length bin to even bin for plotting
Congm12 Oct 30, 2023
b3ca9f9
fix an edge case in converting variable length bin to even bin for pl…
Congm12 Oct 30, 2023
52959ce
merge from devrdr
Congm12 Nov 1, 2023
61fcc31
Create LICENSE
balabanmetin Nov 1, 2023
2fe341b
turn genetic map an input panel; update readme
Congm12 Nov 2, 2023
c2522ef
Merge branch 'main' of github.com:raphael-group/CalicoST
Congm12 Nov 2, 2023
c8ff74b
fix a bug related to genetic map file
Congm12 Nov 2, 2023
9595aaf
clean the rdr parsing functions
Congm12 Nov 7, 2023
af49274
add snakemake for snp parsing; update readme
Congm12 Nov 7, 2023
daebfd7
update readme
Congm12 Nov 7, 2023
d2cb832
organize directory structure; test running calicost in snakemake
Congm12 Nov 8, 2023
090266a
finished snakemake pipeline
Congm12 Nov 13, 2023
fff7fe4
update readme
Congm12 Nov 13, 2023
13a63e1
add example to run on a simulated data
Congm12 Nov 13, 2023
8df90fd
update google drive link and partial output spec
Congm12 Nov 13, 2023
37b2614
add more output spec
Congm12 Nov 13, 2023
6809aae
clean up a few unused files
Congm12 Nov 13, 2023
137a31b
remove prefix in conda environment
Congm12 Nov 13, 2023
7bdac2e
update readme on the test run of simulation
Congm12 Nov 13, 2023
4f0fe12
update readme and setup for dependencies
Congm12 Nov 14, 2023
64e1a55
add system requirements and runtime on example data
Congm12 Nov 14, 2023
aab0b07
remove redundant sorting in merge_bamfile
Congm12 Nov 14, 2023
0a47446
change the directory structure and allow user-input snp directory
Congm12 Nov 14, 2023
312af50
update parameter specification
Congm12 Nov 16, 2023
9c217b8
update default parameter for phasing
Congm12 Nov 29, 2023
0d2dd19
add functions for normal identification and tumor proportion estimation
Congm12 Nov 29, 2023
6b993c6
update tumor proportion estimation function
Congm12 Nov 30, 2023
31daf8e
add inferring tumor proportion module (identify LOH states, estimate …
Congm12 Dec 6, 2023
06e649c
fix bug in loh states detection
Congm12 Dec 7, 2023
4641086
update utils/plot_hatchet import step using calicost installation
Congm12 Dec 7, 2023
8291613
estimate tumor proportion using LOH
Congm12 Dec 30, 2023
7603f20
update the high-purity clone and loh state selection threshold, now u…
Congm12 Jan 20, 2024
ebebf41
add smoothing in tumor proportion estimatino
Congm12 Jan 23, 2024
d0ad5d0
add BAF-only plotting function; fix edge case of exiting
Congm12 Jan 23, 2024
b515bf5
include a user-parameter that was omitted before
Congm12 Jan 23, 2024
43b1a48
minor adjustment on plotting and input parsing
Congm12 Feb 5, 2024
376bbdb
remove redundant code in estimate tumor proportion
Congm12 Feb 15, 2024
6fa1512
make the chr id non-overlapping in copy number plot
Congm12 Feb 15, 2024
cda21a7
add a general code for diffusion model
Congm12 Feb 17, 2024
e737fe3
add a notebook for prostate data
Congm12 Feb 17, 2024
3693c8b
test iframe to show pdf
Congm12 Feb 17, 2024
6d240f3
try another visualization of pdf in notebook; update google drive lin…
Congm12 Feb 17, 2024
1a386b4
update setup to include ete3
Congm12 Feb 18, 2024
f195c3e
readthedocs files
Congm12 Feb 18, 2024
fb3da35
update conf
Congm12 Feb 18, 2024
c7ab19c
version of readthedocs.yaml
Congm12 Feb 18, 2024
b635397
merge change
Congm12 Feb 19, 2024
94db407
update docs
Congm12 Feb 19, 2024
be9be3b
add random initialization selection
Congm12 Feb 20, 2024
bc62fcd
add simulated tutorial
Congm12 Feb 20, 2024
5b2e916
add tutorial to readthedocs
Congm12 Feb 20, 2024
4d2ad0c
move default parsing params to input configurations
Congm12 Feb 26, 2024
c7f1e6c
add example data to github
Congm12 Feb 26, 2024
bd5e8c4
update readme paths for example data
Congm12 Mar 3, 2024
da36c56
fix an edge case
Congm12 Mar 15, 2024
d736db0
simplify environment
Congm12 Apr 11, 2024
358511d
separate installation into parts
Congm12 Apr 11, 2024
850fe1c
remove example paths
Congm12 Apr 12, 2024
47e7917
separate preprocessing from other runs
Congm12 Apr 12, 2024
c8ba107
include example parameter configuration file and some reference files
Congm12 Apr 12, 2024
4d52206
add citation
Congm12 Apr 12, 2024
f4a62fa
update requirement for output_dir
Congm12 Apr 14, 2024
d938107
source for panels
Congm12 Apr 14, 2024
bab0cac
updated example data and tutorial
Congm12 Apr 14, 2024
896c8a0
configuration for multiple slices
Congm12 Apr 14, 2024
201d6d2
url for simulation
Congm12 Apr 14, 2024
d5f1a1e
fix git clone link
Congm12 Apr 14, 2024
5fc50e4
test
Congm12 Apr 14, 2024
e0eefda
Revert "test"
Congm12 Apr 14, 2024
8823977
update doc
Congm12 Apr 14, 2024
38f5d4c
update example
Congm12 Apr 15, 2024
4c7f960
update dpc
Congm12 Apr 15, 2024
380983e
clean preprocessing and argparse
Congm12 Jun 9, 2024
4696325
Merge pull request #3 from raphael-group/cleanprep
Congm12 Jun 9, 2024
88f6c61
a more stable version of converting NB mean and dispersion to n and p…
Congm12 Jul 9, 2024
e52a69e
switch to the more stable version in distribution fitting fun
Congm12 Jul 11, 2024
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129 changes: 129 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,129 @@
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
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# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/
21 changes: 21 additions & 0 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
version: 2

build:
os: ubuntu-22.04
tools:
python: "3.10"

sphinx:
builder: html
configuration: docs/conf.py
fail_on_warning: false

python:
install:
- method: pip
path: .
extra_requirements: [docs]

submodules:
include: [docs/notebooks]
recursive: true
21 changes: 21 additions & 0 deletions GRCh38_resources/HLA_regions.bed
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chr6 29722775 29738528
chr6 29726601 29749049
chr6 29826967 29831125
chr6 29941260 29945884
chr6 30489509 30494194
chr6 31268749 31272130
chr6 31269491 31357188
chr6 32439878 32445046
chr6 32517353 32530287
chr6 32578769 32589848
chr6 32628179 32647062
chr6 32659467 32668383
chr6 32659880 32660729
chr6 32741391 32747198
chr6 32756098 32763532
chr6 32812763 32820466
chr6 32934629 32941028
chr6 32948613 32969094
chr6 33004182 33009591
chr6 33064569 33080775
chr6 33075990 33089696
Binary file added GRCh38_resources/genetic_map_GRCh38_merged.tab.gz
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