It doesn't seem like the documentation has been updated for Salmon 1.0.0, despite the fact that the it says it's the latest version. For example, it still says to build a decoy-aware transcriptome with generateDecoyTranscriptome.sh, and the README points to SalmonTools. This page does have a NOTE at the end pointing to the new tutorial for adding the entire genome as the decoy, as does Salmon's ma

The documentation on readthedocs is not super helpful and the notebook is also not extremely explanatory. A case study on seed labelling would be much more suitable.

See here about inheritance: all common parameters must be moved to the first chunk.

Clarify, which methods can be called multiple times (like findCommunities), and which can not (buildGraph).

The code style is fairly inconsistent across files in terms of indentation, spacing, brace placement etc. The easiest way to resolve is to agree on a style guide (eg, google's for C++ and tidyverse's for R) and periodically apply a code styling tool (eg, Astyle for C++ or [

If you accidentally provide a ill-formatted configuration file (such as forgetting to specify the config and resulting in the first file being considered the config), you get a confusing error message:

input/sample.fq.tagged.1.tophat/accepted_hits.bam(1): expected <

An message like 'Error processing configuration file', would be must more useful.

We need documentation of APIs. Since users need to know the options of each function, the data structures, in order to fine-tune their pipeline or skip certain steps. Currently, the only available documentation is the tutorial, which is not enough.

Hello,

FYI due to hpcng/singularity#3401

building the container fail with singularity 3.5.2 due to

%post -c /bin/bash

OK with singularity 3.4.0 and 3.5.3 not tested with 3.2*

regards

Eric

Silhouette plot labels clusters by integers from 1 - # of clusters. If clusters are named, or numbered differently (Seurat counts clusters from zero because apparently they forgot they weren't Python?), this creates a great deal of confusion.

ERROR: Could not find a version that satisfies the requirement tensorflow==1.7.0 (from desc) (from versions: 1.13.0rc1, 1.13.0rc2, 1.13.1, 1.13.2, 1.14.0rc0, 1.14.0rc1, 1.14.0, 1.15.0rc0, 1.15.0rc1, 2.0.0a0, 2.0.0b0, 2.0.0b1, 2.0.0rc0, 2.0.0rc1, 2.0.0rc2)
ERROR: No matching distribution found for tensorflow==1.7.0 (from desc)

10X released a dataset of ~100K CD8 T Cells, we should make an example notebook working with this data. We need to be careful to not add too much data to this repo however. Make a branch for this.

Dataset link: https://www.10xgenomics.com/extra/#whats-new?utm_source=Twitter&utm_medium=&utm_content=&utm_campaign=2019-Social-Twitter

https://support.10xgenomics.com/single-cell-vdj/datasets/3.0