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Vivek Bhardwaj vivekbhr Hubrecht Institute the Netherlands https://vivekbhr.github.io Computational Biology Researcher at Hubrecht Institute, the Netherlands.

deeptools/pyGenomeTracks 525

python module to plot beautiful and highly customizable genome browser tracks

deeptools/deepTools 493

Tools to process and analyze deep sequencing data.

deeptools/HiCExplorer 143

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

BuysDB/SingleCellMultiOmics 12

Tools which deal with multiple single cell measurements

deeptools/HiCBrowser 11

Simple web browser to visualize HiC tracks

friedue/AlleleSpecific 2

pipeline for allele-specific mapping of short reads

vivekbhr/cage_pipeline 2

Pipeline for CAGE data analysis using icetea

vivekbhr/icetea 2

R/Bioconductor package for analysis of single and paired-end capped-RNAseq data (CAGE/RAMPAGE/MAPCap)

friedue/Clustering 1

collection of scripts used for Chelmicki and Duendar et al. 2014

issue commentdeeptools/deepTools

Issue with computeMatrix/plotProfile (deepTools/2.4.0) using multiple region files

@ANDdna1991 they are being skipped as they don't have any reads (or no reads counted after considering your criteria). You can try the --missingDataAsZero without the skipZeros option to keep those

zsun89

comment created time in a month

issue openedvivekbhr/scRIApipe

$tempdir

Add the TMPDIR env variable for the get_counts step, the workflow fails sometimes due to the tempdir being full

created time in a month

startedrob-p/FQFeeder

started time in 2 months

issue closedDaehwanKimLab/hisat2

Allow reporting one of the sam tags in `hisat-3n-table`

Hi @DaehwanKimLab20191011

This tool looks really great as a replacement to bismark and others! I am looking at single-cell BS-seq data and I am appending the BC/CB tag in the alignments. Would you consider reporting the value of a user-specified SAM tag with hisat-3n-table (as another column) so I can get the corresponding cell barcode tag in the output table?

Thanks! Vivek

closed time in 2 months

vivekbhr

issue commentDaehwanKimLab/hisat2

Allow reporting one of the sam tags in `hisat-3n-table`

This sounds good. Thanks Leo! :+1:

vivekbhr

comment created time in 2 months

issue commentDaehwanKimLab/hisat2

Allow reporting one of the sam tags in `hisat-3n-table`

Hi Leo Thanks for the quick reply. I see that could be an issue. So is there any efficient solution to this? Or would you rather suggest splitting the BAM files by cell barcode before running the hisat-3n-table command (that would be a mess but would work for now)?

vivekbhr

comment created time in 2 months

issue openedDaehwanKimLab/hisat2

Allow reporting one of the sam tags in `hisat-3n-table`

Hi @DaehwanKimLab20191011

This tool looks really great as a replacement to bismark and others! I am looking at single-cell BS-seq data and I am appending the BC/CB tag in the alignments. Would you consider reporting the value of a user-specified SAM tag with hisat-3n-table (as another column) so I can get the corresponding cell barcode tag in the output table?

Thanks! Vivek

created time in 2 months

issue commentvtraag/leidenalg

optimise_partition_multiplex: how to get the layer:partition mapping

Got it, so I just have to take out the name and time attribute from any of the partitions after I run optimise_partition_multiplex. Just checked it and indeed the attributes are there in my case. :+1:

vivekbhr

comment created time in 3 months

issue openedvtraag/leidenalg

optimise_partition_multiplex: how to get the layer:partition mapping

Hi @vtraag . I ran optimise_partition_multiplex on a 3 layer graph and get 30 communities. After this, I see that some of the nodes are in multiple communities, and therefore some nodes are also present multiple times in the output partition object. Now I assume that this is due to these nodes having different memberships in different layers, but how do I get the layer:membership mapping for these nodes?

My partition type is leidenalg.VertexPartition.ModularityVertexPartition.

Thanks in advance

created time in 3 months

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