Davide Cittaro

SAM output broken

10

Hi all, I understand SAM output is not optimized and it is discouraged, however I had to test it and I run into some issues. First of all, output is...

Counts over a given bed file

10

Hi all, I'm testing `chromap` and I'd say I'm impressed by the performances. In addition to the current options, would you consider the possibility to output counts over given intervals?...

Hi there, I'm trying to use skfusion with my data, but I feel there is so little documentation describing functions and object types. I'm doing a little of reverse engineering...

Again on insulation scores

3

Hi all, I'm trying again to interpret insulation scores from hicFindTAD, which I understand is not the one described [here](https://www.nature.com/articles/s41467-018-03017-1#Sec12) or [here](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3387-6). Looking at the code I found this should...

UnboundLocalError when using design matrix

4

I'm trying to use a design matrix to run a simple test, in place of a formula but I cannot use due to this error: ``` >>> dmat_flat = de.utils.design_matrix(data...

Core dump with continuous covariates

2

Good morning, I'm trying to test differential expression according to a model with three continuous independent variables (here `A`, `B` and `C`). Since I'm interested in all coefficients, I'm doing...

Intersect library fragments and not alignment in multibamcov

1

I've added an option to multiBamCov which extends one read (R1, right now) for properly paired alignments to the size of ISIZE before the intersection with the bed file. This...

plot_distance_vs_interactions issue

1

Hi again, During the tests I'm running, I've slipped into this error from `plot_distance_vs_interactions` function ``` ddi = plot_distance_vs_interactions(reads, savefig='DDI.png', axe = ax, max_diff=10000, resolution=1000000) Traceback (most recent call last):...

I'm trying to apply mnn on my data, basically following the README of this project, but ```python corrected = mnnpy.mnn_correct(*tn5_data_list, batch_categories=batches) Traceback (most recent call last): File "", line 1,...

Error when running sparse Robust PCA

7

#### Describe the bug Computation of sparse robust pca crashes as it calls svd with unexpected keyword (`full_matrices`) #### Steps or Code to Reproduce Mostly copied from tensorly docs ```python...