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Last updated: 2026-07-29

Checks: 1 1

Knit directory: misc/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: uncommitted changes

The R Markdown file has staged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: a2769cb

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version a2769cb. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .claude/
    Ignored:    GSE87571/
    Ignored:    analysis/.RData
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/ALStruct_cache/
    Ignored:    analysis/ebproj_01.html
    Ignored:    data/.Rhistory
    Ignored:    data/methylation-data-for-matthew.rds
    Ignored:    data/pbmc/
    Ignored:    data/pbmc_purified.RData

Untracked files:
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Unstaged changes:
    Modified:   .gitignore
    Modified:   analysis/eb_snmu.Rmd
    Modified:   analysis/ebnm_binormal.Rmd
    Modified:   analysis/ebpower.Rmd
    Modified:   analysis/fastICA_asymmetric.Rmd
    Modified:   analysis/flashier_log1p.Rmd
    Modified:   analysis/flashier_sla_text.Rmd
    Modified:   analysis/logistic_z_scores.Rmd
    Modified:   analysis/mr_ash_pen.Rmd
    Modified:   analysis/nmu_em.Rmd
    Modified:   analysis/susie_flash.Rmd
    Modified:   analysis/tap_free_energy.Rmd
    Modified:   misc.Rproj

Staged changes:
    New:        analysis/fastICA_asymmetric.Rmd
    Modified:   analysis/index.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	a2769cb	Matthew Stephens	2026-07-17	Build site.
Rmd	42fc276	Matthew Stephens	2026-07-17	Add fastica_precondition to index
html	f33b4cb	Matthew Stephens	2026-07-17	Build site.
Rmd	664e40e	Matthew Stephens	2026-07-17	Add link to fastica_nonwhitened
html	3e9f509	Matthew Stephens	2026-07-16	Build site.
Rmd	68bd08b	Matthew Stephens	2026-07-16	Add fastica_skew to index
html	1333f4f	Matthew Stephens	2026-06-22	Build site.
Rmd	ee9f0e9	Matthew Stephens	2026-06-22	workflowr::wflow_publish("index.Rmd")
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Rmd	dd97713	Matthew Stephens	2026-05-06	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	2578a9c	Matthew Stephens	2026-05-04	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	2960b63	Matthew Stephens	2025-11-16	workflowr::wflow_publish("index.Rmd")
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Rmd	7aaf2cc	Matthew Stephens	2025-11-03	workflowr::wflow_publish("index.Rmd")
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Rmd	34ab198	Matthew Stephens	2025-07-31	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	099a0c1	Matthew Stephens	2025-03-12	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	c00f72c	Matthew Stephens	2025-03-12	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	83c79a0	Matthew Stephens	2025-03-09	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	232b913	Matthew Stephens	2025-02-27	workflowr::wflow_publish("index.Rmd")
html	86c66e9	Matthew Stephens	2025-02-27	Build site.
Rmd	5cd9254	Matthew Stephens	2025-02-27	workflowr::wflow_publish("index.Rmd")
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Rmd	04d7bed	Matthew Stephens	2024-11-11	workflowr::wflow_publish("index.Rmd")
html	80071e2	Matthew Stephens	2024-09-14	Build site.
Rmd	c95b0e1	Matthew Stephens	2024-09-14	workflowr::wflow_publish("analysis/index.Rmd")
html	d75571b	Matthew Stephens	2024-07-03	Build site.
Rmd	03ccdd5	Matthew Stephens	2024-07-03	workflowr::wflow_publish("index.Rmd")
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Rmd	6f3bc4e	Matthew Stephens	2024-05-01	workflowr::wflow_publish("index.Rmd")
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Rmd	a30976c	Matthew Stephens	2024-04-04	workflowr::wflow_publish("index.Rmd")
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Rmd	e5e386d	Matthew Stephens	2024-02-21	workflowr::wflow_publish("index.Rmd")
html	681a57b	Matthew Stephens	2023-11-11	Build site.
Rmd	52387ae	Matthew Stephens	2023-11-11	workflowr::wflow_publish("index.Rmd")
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Rmd	70a20ae	Matthew Stephens	2023-11-10	workflowr::wflow_publish("index.Rmd")
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Rmd	eef47ef	Matthew Stephens	2023-11-07	workflowr::wflow_publish("index.Rmd")
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Rmd	7d152f4	Matthew Stephens	2023-10-27	workflowr::wflow_publish("analysis/index.Rmd")
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Rmd	96b38d1	Matthew Stephens	2023-10-13	workflowr::wflow_publish("analysis/index.Rmd")
html	2cd999c	Matthew Stephens	2021-10-25	Build site.
Rmd	0552fee	Matthew Stephens	2021-10-25	workflowr::wflow_publish("index.Rmd")
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Rmd	2ebd0bf	Matthew Stephens	2021-10-21	workflowr::wflow_publish("index.Rmd")
html	cbd45f1	Matthew Stephens	2021-10-21	Build site.
Rmd	56f168b	Matthew Stephens	2021-10-21	workflowr::wflow_publish("index.Rmd")
html	bf18633	Matthew Stephens	2021-07-29	Build site.
Rmd	0b3b1bd	Matthew Stephens	2021-07-29	workflowr::wflow_publish("analysis/index.Rmd")
html	e9d380a	Matthew Stephens	2021-05-26	Build site.
Rmd	dc33cf7	Matthew Stephens	2021-05-26	wflow_publish("index.Rmd")
html	bc1710f	Matthew Stephens	2021-05-22	Build site.
Rmd	123ac2a	Matthew Stephens	2021-05-22	workflowr::wflow_publish("index.Rmd")
html	e9ea050	Matthew Stephens	2021-05-22	Build site.
html	a18dde3	Matthew Stephens	2021-05-22	Build site.
Rmd	a63c7cf	Matthew Stephens	2021-05-22	workflowr::wflow_publish("index.Rmd")
html	1223cbf	Matthew Stephens	2021-05-11	Build site.
Rmd	8d7e6b2	Matthew Stephens	2021-05-11	wflow_publish("analysis/index.Rmd")
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Rmd	bbeb8fe	Matthew Stephens	2021-03-29	workflowr::wflow_publish("index.Rmd")
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Rmd	d95180c	Matthew Stephens	2021-02-17	workflowr::wflow_publish("index.Rmd")
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Rmd	3664ae9	Matthew Stephens	2021-02-04	wflow_publish("index.Rmd")
html	b0fc283	Matthew Stephens	2021-01-23	Build site.
Rmd	22247d8	Matthew Stephens	2021-01-23	workflowr::wflow_publish("index.Rmd")
html	3514864	Matthew Stephens	2020-11-05	Build site.
Rmd	25fe3ba	Matthew Stephens	2020-11-05	workflowr::wflow_publish("index.Rmd")
html	12e6582	Matthew Stephens	2020-10-09	Build site.
Rmd	83a0d5b	Matthew Stephens	2020-10-09	workflowr::wflow_publish("index.Rmd")
html	d68ffe1	Matthew Stephens	2020-10-09	Build site.
Rmd	aff82bf	Matthew Stephens	2020-10-09	workflowr::wflow_publish("index.Rmd")
html	c058881	Matthew Stephens	2020-08-10	Build site.
Rmd	04265da	Matthew Stephens	2020-08-10	workflowr::wflow_publish("index.Rmd")
html	3b956ac	Matthew Stephens	2020-08-03	Build site.
Rmd	3f739e6	Matthew Stephens	2020-08-03	workflowr::wflow_publish("index.Rmd")
html	2020f8d	Matthew Stephens	2020-07-20	Build site.
Rmd	1f42629	Matthew Stephens	2020-07-20	workflowr::wflow_publish("index.Rmd")
html	e74f8d1	Matthew Stephens	2020-06-29	Build site.
Rmd	f100079	Matthew Stephens	2020-06-29	workflowr::wflow_publish("index.Rmd")
html	b9e0d03	Matthew Stephens	2020-06-26	Build site.
Rmd	8098b13	Matthew Stephens	2020-06-26	workflowr::wflow_publish("index.Rmd")
html	60d5a2a	Matthew Stephens	2020-06-22	Build site.
Rmd	de094ed	Matthew Stephens	2020-06-22	workflowr::wflow_publish("index.Rmd")
html	8ffcdbe	Matthew Stephens	2020-06-12	Build site.
Rmd	64783b0	Matthew Stephens	2020-06-12	workflowr::wflow_publish("index.Rmd")
html	f013116	Matthew Stephens	2020-06-04	Build site.
Rmd	6119265	Matthew Stephens	2020-06-04	workflowr::wflow_publish("index.Rmd")
html	e77a3da	Matthew Stephens	2020-06-02	Build site.
Rmd	494efd6	Matthew Stephens	2020-06-02	workflowr::wflow_publish("index.Rmd")
html	cd477e2	Matthew Stephens	2020-05-29	Build site.
Rmd	8fda376	Matthew Stephens	2020-05-29	workflowr::wflow_publish("index.Rmd")
html	1782e1f	Matthew Stephens	2020-05-20	Build site.
Rmd	55fc29f	Matthew Stephens	2020-05-20	wflow_publish("index.Rmd")
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Rmd	6319251	Matthew Stephens	2020-05-05	wflow_publish("index.Rmd")
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Rmd	22b6c82	Matthew Stephens	2020-03-12	workflowr::wflow_publish("index.Rmd")
html	7b14fa1	Matthew Stephens	2020-03-06	Build site.
Rmd	729fd24	Matthew Stephens	2020-03-06	workflowr::wflow_publish("../analysis/index.Rmd")
html	48994fe	Matthew Stephens	2020-03-06	Build site.
Rmd	3f4de46	Matthew Stephens	2020-03-06	workflowr::wflow_publish("../analysis/index.Rmd")
html	21a3a6b	Matthew Stephens	2019-12-04	Build site.
Rmd	74acef9	Matthew Stephens	2019-12-04	workflowr::wflow_publish("index.Rmd")
html	c193a6c	Matthew Stephens	2019-11-02	Build site.
Rmd	503bea4	Matthew Stephens	2019-11-02	workflowr::wflow_publish("index.Rmd")
html	82888f7	Matthew Stephens	2019-10-30	Build site.
Rmd	0fcce3b	Matthew Stephens	2019-10-30	wflow_publish("index.Rmd")
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html	b18efff	Matthew Stephens	2019-10-18	Build site.
Rmd	b2b61c3	Matthew Stephens	2019-10-18	workflowr::wflow_publish("index.Rmd")
html	c4d9e65	Matthew Stephens	2019-10-12	Build site.
Rmd	35852bd	Matthew Stephens	2019-10-12	wflow_publish("index.Rmd")
html	049385b	Matthew Stephens	2019-10-07	Build site.
Rmd	65fe6b5	Matthew Stephens	2019-10-07	workflowr::wflow_publish("index.Rmd")
html	dcd23f8	Matthew Stephens	2019-10-05	Build site.
Rmd	94427a3	Matthew Stephens	2019-10-05	wflow_publish("index.Rmd")
html	b472719	Matthew Stephens	2019-07-15	Build site.
Rmd	960db08	Matthew Stephens	2019-07-15	wflow_publish("index.Rmd")
html	f0eac95	Matthew Stephens	2019-06-25	Build site.
Rmd	0bfd902	Matthew Stephens	2019-06-25	workflowr::wflow_publish("analysis/index.Rmd")
html	26c3722	Matthew Stephens	2019-05-10	Build site.
Rmd	dbf0b7a	Matthew Stephens	2019-05-10	workflowr::wflow_publish("index.Rmd")
html	649a290	Matthew Stephens	2019-05-10	Build site.
Rmd	278af42	Matthew Stephens	2019-05-10	workflowr::wflow_publish("index.Rmd")
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---

This repo is my “catch-all” for putting things in that may relate to various ongoing projects.

Ash

• Null simulations with larger n=13500
• NPMLE with larger n=100000
• Examine the delta operator for ash
• Ash on poisson data

Mr Ash

• implementing mr ash as a penalized method
• coordinate ascent and parallel version
• mr.ash.alpha applied to changepoint problems
• combining mr.ash and ridge regression/iterative ridge regression
• bimodal example from “Bayesian lasso”" paper
• mr ash vs lasso: example where lasso does better
• mr ash vs lasso: follow-up checking objective fn
• lasso vs ridge: follow-up checking p=1000 vs p=2000
• Debugging and scaling

Ridge Regression

• Ridge regression for trend filtering

• Ridge regression via conjugate gradient

• EM for hyperparameters Ridge regression

• EM for hyperparameters of Ridge regression using SVD

• EM for hyperparameters of Ridge regression - convergence issue

• ADMM for ridge regression with heterogenous prior variances

• Sloppy ADMM

Lasso

• Fit lasso by EM
• teach myself ADMM (L1 and L0)
• check scaling of glmnet with n

EBMR

• An initially suprising overfitting result for EB lasso
• An illustration of ebmr with estimated grid

Mash

• Initial mash analysis of RBC z scores
• Comparing the UDI BFs from mash with originals

Mouthwash

• Looking at how Mouthwash deals with t distributions vs normal

Flash

• Illustration of conservative behaviour issue

• Looking at differentiating the likelihood at the null

• Apply SSVD to GTEX data

• Method of moments for EbayesThresh

• flashier run on stocks data

• Notes on a sparse PCA objective function

• Notes on the log1p transform for count/Poisson data

• Approximating Poisson likelihood by normal, with log1p transform

• Initial runs of flashier on text data

• Flashier semi-NMF on text data

• Try at using shifted exponential prior in flashier (did not work as I expected)

NMF

• Try NMF on a simple simulation with sparse factors
• Run NMF on covariance matrices, including tree-like case
• Non-negative matrix underapproximation via EM
• A power method for fitting symmetric NMF
• An EB version of the power method for symmetric NMF

ICA

• Initial try of fastICA on simulated data

• Single unit fastICA on simulated data

• Single unit fastICA with centering, to help find asymmetric binary groups (flawed)

• Single unit fastICA with intercept, to help find asymmetric binary groups

• FastICA with tilted log-cosh contrast for skewed/sparse binary sources

• FastICA for non-whitened data: exact equivariance and initialization bias

• Preconditioned FastICA: homotopy method and TLC contrast

• EB FastICA with asymmetric prior: alternating optimization for sparse sources

• EBproj: quasi-Newton with binary prior and Section-5 sigma (Test 1)

• Motivated by ICA, I try a flash+low-rank approach

• Motivated by ICA, I try an EB approach to find subspaces

Multinomial factor models

• Possible version of structure/admixture with sparsity via ARD-like prior

Weighted SVD

• Outline of EM algorithm for fitting weighted SVD
• Investigation of weighted SVD for Poisson data
• Brief experiment with primePCA
• Example of convergence problem in softimpute

Finemapping

• Comparison of varbvs and varbvsmix
• A simple approach to fine mapping
• A new VB approach
• Connect new VB to single SNP Bayesian analysis
• selective inference on toy example
• selective inference with correlated variables
• hierarchical inference example

Logistic regression

• Logistic regression z scores decrease as effect size increases

LD score regression

• An initial look at XtX (Sigma)^{-1}

Missing Data in regression

• Pseudo-data idea
• Approximate Inference with missing data

Approximate message passing and related

• Compare precision and covariance for ridge regression
• Initial try of VAMP

Depletion

• Using ash for depletion

Single cell data

• explore t test on log-transformed data
• initial play with sinkhorn normalization
• flashier on pbmc_purified data

flash-drift

• look at SVD applied to tree structured data
• Eigen-decomposition applied to some simple 4- and 8-tip trees
• Apply sparsepca and flash to some tree data
• Look at effect of size of first factor on flash
• Flash-cov on overlapping groups
• A look at estimates of the latent factors on trees
• Outline of a method for building trees topdown using flash
• Some results for trees and overlapping groups, initializing using point-laplace

EBNM

• A bimodal mixture of 2 normals ebnm function

IRLS

• implementation of irls for logistic regression