Benjamin Yeh

Improve compatibility with Anki 2.1.41+

1

Fixes RL button to correctly insert `class="shuffle"` into `` element, thereby allowing shuffling to work correctly in Anki 2.1.41+, which [requires](https://forums.ankiweb.net/t/add-on-porting-notes-for-anki-2-1-41/7390) using `.getSelection()` on a _field_ instead of `window`. This...

```r library(Cardinal) set.seed(20) mse

Consider the following code snippet. `Cardinal::image()` works fine if called from the global environment. ```r library(Cardinal) set.seed(200) mse

intensityData(object) <- value, peakData(object) <- value methods are broken

1

The setter method `intensityData(object)

Looking over the source code, it appears that `LoadEdgeList()` and `LoadEdgeListStr()` are supposed to support compressed files with filenames ending in .gz, .7z, .rar, .zip, .cab, .arj, .bzip2, and .bz2...

Incorrect derivative of function w.r.t. parameterized argument alpha

2

This footnote is not quite right. https://github.com/distillpub/post--attribution-baselines/blob/765dadd4c57418962cdf6056094121f630569645/public/index.html#L267-L278 `$$\gamma(\alpha)$$` is a vector, so by the multivariable chain rule, ``` $$ \frac{\delta f(\gamma(\alpha))}{\delta \alpha} = \sum_i \frac{\delta f(\gamma(\alpha))}{\delta \gamma_i} \times \frac{\delta \gamma_i(\alpha)}{\delta...

Is the order of unnamed (positional) input files preserved by {input}?

2

Here's a minimal Snakefile demonstrating my question: ``` FILES = {'sample1': ['a.bed', 'b.bed', 'c.bed']} rule all: input: "sample1.out" rule rule1: input: lambda wildcards: FILES[wildcards.sample] output: "{sample}.out" shell: ''' echo {input:q}...

Documentation: Missing test files and errors when running commands from tutorial

1

The "Advanced Step-by-step peak calling using MACS3 commands" tutorial [[webpage](https://macs3-project.github.io/MACS/docs/Advanced_Step-by-step_Peak_Calling.html), [source](https://github.com/macs3-project/MACS/blob/master/docs/source/docs/Advanced_Step-by-step_Peak_Calling.md)] has 2 issues: 1. The tutorial claims that the 2 test files, CTCF_ChIP_200K.bed.gz and CTCF_Control_200K.bed.gz, can be found "in...

The last Bowtie 2 update that specifically addressed SAM format versions was bowtie 2.4.5, which adopted support for SAM version 1.5. (Bowtie 2 currently generates SAM headers `@HD VN:1.5`.) The...

Use canonical calloc arguments order for parsed_opts_t allocation

1

This commit should NOT produce any change in behavior; swapping the order of the arguments to `calloc()` does NOT affect the behavior of `calloc()`. Thus, the main purpose of this...