sahil seth

reverse chronological order

5

This is a awesome list! I follow and read through it off and on. Since the number of articles have really grown and would continue to grow. Would you like...

R console, within jupyter notebook

3

Before submitting an issue please be sure to answer these questions with **yes**: - [x] Did you follow the [official installation instructions](https://irkernel.github.io/installation/)? yes - [x] Did you reproduce the error...

Extracting AF from sample specific coloumns

1

Is it possible to specify the `name` of the tumor sample in the VCF, and then for pcgr to extract `AF`, `DP` from that column? Do you a recommended approach,...

``` flowr kill x=runs/bam_mutect-HCC1143___HCC1143_BL-20160413-21-* found multiple wds: runs/bam_mutect-HCC1143___HCC1143_BL-20160413-21-52-53-VhvZDq9L runs/bam_mutect-HCC1143___HCC1143_BL-20160413-21-54-49-abhTg3DJ If you want to kill all of them, kill again with force=TRUE flowr kill x=runs/bam_mutect-HCC1143___HCC1143_BL-20160413-21* found multiple wds: runs/bam_mutect-HCC1143___HCC1143_BL-20160413-21-52-53-VhvZDq9L runs/bam_mutect-HCC1143___HCC1143_BL-20160413-21-54-49-abhTg3DJ runs/bam_mutect-HCC1143___HCC1143_BL-20160413-22-07-02-kNZqOJ9W...

Simplify the configuration setup

1

In two subsequent versions of flowr, remove extra folders from where configuration file are loaded. By default all configuration is loaded using `.flowr` file from the home dir. Other than...

If conf files cannot be loaded properly, die gracefully. The following error is quite confusing: ``` library(flowr) Loading required package: params Loading required package: whisker Flowr: streamlining workflows Error :...

Currently, in flowr (like many other tools), all parameters are decided before execution. There are a few use cases in which it might be useful, that step A; analyzes the...

The initial flow_details.txt file does not have a started column. When one runs flowr::status, it adds this column to the file. Some downstream functions expect this column to be present,...

Corrected NEUT call, which seems to be a region of DLOH instead.

1

Hi @gavinha: I have this region, which seems to be LOH based on GATK-CNV and titan call, however, upon correction it becomes NEUT (`chr2:196889180;242814009`). Guess I am missing something, but...

py$start thowing a error regarding connection not open

2

First, each time I need a new functionality in knitr and search, I see Yihui already has it! Runr is very cool and promising. I am trying to create Rmd...