User James Hawley

16 votes

Accepted

Ultimate reproducibility in R?

answered Aug 31, 2017 at 15:35

9 votes

Accepted

Can't install newest Blast from Conda

answered Nov 29, 2018 at 21:22

5 votes

Accepted

'Wildcards' object has no attribute 'sample'

answered Jan 14, 2019 at 23:37

5 votes

Accepted

How many types of DNA methylation are there?

answered Oct 11, 2019 at 15:24

4 votes

Doubt about using TPM for statistics

answered Mar 16, 2021 at 21:37

4 votes

How to identify which isoforms of a gene are actually expressed in my data?

answered Jul 19, 2022 at 17:57

4 votes

How to differentiate DNA fastq and RNA fastq files?

answered Apr 1 at 20:34

3 votes

Accepted

ATAC peak anatations

answered May 6, 2022 at 15:47

3 votes

Using `install.packages` with conda-managed R

answered Jul 12, 2019 at 17:07

3 votes

How to subset a BAM by a list of QNAMEs?

answered Sep 27, 2019 at 13:32

2 votes

Biological replicates on Chip-seq Transcription factor data

answered Jul 25, 2019 at 20:07

2 votes

Accepted

Get a single number representing the contact probability between a pair of genomic loci using HiC data

answered May 7, 2020 at 19:43

2 votes

Accepted

How to split FASTQ reads without re-running `fastq-dump`?

answered May 8, 2020 at 14:29

2 votes

Install DESeq2 through anaconda

answered Nov 29, 2018 at 20:48

2 votes

Score predefined ChIP-seq peaks with MACS2 or equivalent

answered Nov 29, 2018 at 20:59

2 votes

Accepted

Different results of spearman correlation between TPM and FPKM

answered Jun 16, 2022 at 21:59

2 votes

How does picard's MarkDuplicate handle unmapped reads?

answered Jul 20, 2020 at 22:58

2 votes

Accepted

Advantages of paired-end sequencing compared to single end

answered Sep 21, 2020 at 19:27

2 votes

beginner RNA-seq Replicate papers

answered Jun 20, 2022 at 13:43

2 votes

Methylation data: beta values are normally distributed

answered Sep 9, 2022 at 16:50

1 vote

Is loss/gain of function reflected in RNA-seq transcript counts?

answered Sep 10, 2022 at 16:41

1 vote

How to visualize genome track of gene in specific cell-lines?

answered Oct 27, 2022 at 14:31

1 vote

Accepted

How to get the intersection of peaks after peak calling using MACS2?

answered Mar 10, 2020 at 16:25

1 vote

I am trying to find correlation between two ChIP-seq datasets but the Pearson and Spearman test results do not correspond with the peak overlap

answered Apr 19 at 14:59

1 vote

snakemake restricting resources for specific rule

answered May 25 at 12:57

1 vote

Recommended coverage depth for ChIP Seq (H3K9me3 )

answered Oct 13, 2020 at 1:26

1 vote

Why are TPMs per 10k or 100k in many scRNA-seq studies?

answered Mar 10, 2021 at 17:43

1 vote

Accepted

Clarification about how mapping to a reference genome works in RNA seq

answered Jun 9, 2020 at 22:27

1 vote

Accepted

Grouping x-axis in scatter plot

answered Jun 17, 2022 at 17:22

1 vote

Accepted

Normalization methods to combine scRNA-seq experiments with different sequencing depths

answered May 13, 2022 at 20:27

Stack Exchange Network

43 Answers

Ultimate reproducibility in R?

Can't install newest Blast from Conda

'Wildcards' object has no attribute 'sample'

How many types of DNA methylation are there?

Doubt about using TPM for statistics

How to identify which isoforms of a gene are actually expressed in my data?

How to differentiate DNA fastq and RNA fastq files?

ATAC peak anatations

Using `install.packages` with conda-managed R

How to subset a BAM by a list of QNAMEs?

Biological replicates on Chip-seq Transcription factor data

Get a single number representing the contact probability between a pair of genomic loci using HiC data

How to split FASTQ reads without re-running `fastq-dump`?

Install DESeq2 through anaconda

Score predefined ChIP-seq peaks with MACS2 or equivalent

Different results of spearman correlation between TPM and FPKM

How does picard's MarkDuplicate handle unmapped reads?

Advantages of paired-end sequencing compared to single end

beginner RNA-seq Replicate papers

Methylation data: beta values are normally distributed

Is loss/gain of function reflected in RNA-seq transcript counts?

How to visualize genome track of gene in specific cell-lines?

How to get the intersection of peaks after peak calling using MACS2?

I am trying to find correlation between two ChIP-seq datasets but the Pearson and Spearman test results do not correspond with the peak overlap

snakemake restricting resources for specific rule

Recommended coverage depth for ChIP Seq (H3K9me3 )

Why are TPMs per 10k or 100k in many scRNA-seq studies?

Clarification about how mapping to a reference genome works in RNA seq

Grouping x-axis in scatter plot

Normalization methods to combine scRNA-seq experiments with different sequencing depths