Benjamin Schuster-Boeckler

--OT and --OB suggestions by mbias produce "Invalid bounds string"

7

I ran `MethylDackel mbias` on a WGBS file (mapped with bwameth.py) and got: ``` >$ MethylDackel mbias -@ 4 -q 5 -r chr7 hg38.fa GSM4505863_md.bam GSM4505863_mbias_chr7 Suggested inclusion options: --OT...

How to exclude the first 10bp of each read, irrespective of orientation

9

I'm making a separate issue from #101 here since this is not a bug but a question, really: I have a directional library of ~140 bp reads after adapter and...

"Invalid bounds string" with the example setting from the help

6

`MethylDackel extract --help` says: ``` --OT INT,INT,INT,INT Inclusion bounds for methylation calls from reads/pairs originating from the original top strand. Suggested values can be obtained from the MBias program. Each...

Alternatives to consensushc for predict from NMFfitX

1

Hi Renaud, I'm trying to reproduce a clustering similar to the one described in [this paper](http://www.sciencedirect.com/science/article/pii/S2211124712004330). I believe that the first part of their algorithm is identical to a `nmf`...

**Is your feature request related to a problem? Please describe.** I'm trying to use our business Dropbox account to store folders that contain research analysis files. Working in biological data...

.mignore file causes sync error due to new Dropbox business folder structure

5

**Describe the bug** Dropbox recently changed how folders are organised for business accounts. The top-level directory in the dropbox root directory is not writeable to the user any more, but...

Trait bounds of RandomForest::fit conflict with those of predict and other metrics

5

I am trying to perform cross validation of a RandomForest like this: ```rust let cv_score = cross_validate( RandomForestClassifier::new(), x_train, y_train, RandomForestClassifierParameters::default() .with_criterion(SplitCriterion::ClassificationError) .with_n_trees(*n_tree) .with_m(*m_feat) .with_min_samples_split(*m_split) .with_min_samples_leaf(*m_leaf), &KFold::default().with_n_splits(5), &precision ).unwrap(); ```...

Slight confusion about gap costs vs mismatches

2

First of all: thanks for making this great library available! We're using the Rust wrapper in a tool that aligns DNA reads from a custom PacBio analysis. We have a...