User An Ignorant Wanderer

4 votes

1 answer

520 views

Programmatically retrieve Metadata from SRA Run Selector

asked Jun 8, 2021 at 13:22

3 votes

3 answers

3k views

Using bioconductor from Python

asked May 10, 2020 at 14:40

3 votes

1 answer

101 views

Why are asymmetric distributions an issue for GSEA?

asked Mar 21 at 2:13

2 votes

4 answers

519 views

How can I obtain FTP links to studies in ENA given a BioProject ID?

asked Jul 12, 2020 at 23:03

2 votes

2 answers

3k views

Advantages of paired-end sequencing compared to single end

asked Sep 12, 2020 at 15:15

2 votes

1 answer

81 views

GSEA: Computing an Enrichment Score (as described in the original paper)

asked Jul 10, 2021 at 6:48

2 votes

1 answer

132 views

Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data

asked Jun 5, 2020 at 17:08

2 votes

1 answer

150 views

Programmatically retrieve Accession List from NCBI

asked Jul 8, 2020 at 22:46

1 vote

2 answers

308 views

Too many requests error when querying NCBI

asked Jul 9, 2020 at 21:25

1 vote

1 answer

269 views

What is the best way to get a large number of RNA seq data from SRA in Python without being denied access

asked Jul 12, 2020 at 3:45

1 vote

2 answers

404 views

Tools for creating gene coexpression networks

asked May 11, 2020 at 20:59

1 vote

1 answer

280 views

Importing a WGCNA co-expression network into a networkX graph in Python

asked May 12, 2020 at 19:01

1 vote

1 answer

134 views

Loading all PPI information from Uniprot into a graph in NetworkX

asked Apr 11, 2020 at 23:05

1 vote

1 answer

43 views

Weighted Network Analysis Book by Steve Horvath, taking the power of a matrix

asked May 17, 2020 at 0:33

1 vote

2 answers

271 views

How to tell if library generation for RNA-seq experiments are stranded vs not stranded

asked Jun 4, 2020 at 23:42

1 vote

1 answer

46 views

What is a good rule of thumb for the threshold of noise versus signal for RPK in RNA seq?

asked Aug 4, 2020 at 22:56

1 vote

0 answers

190 views

Trying to download a large number of files from ENA programmatically

asked Jul 12, 2020 at 18:17

1 vote

1 answer

677 views

What unit (TPM, FPKM/RPKM, or other) to use when working across samples

asked Jun 7, 2020 at 1:48

1 vote

1 answer

53 views

Can I use a tool for highly variable gene selection for selecting highly variable "bins" from an ATACSeq dataset?

asked Aug 10, 2022 at 17:19

1 vote

1 answer

51 views

What does the "filters" argument in "getBM" do?

asked Nov 5, 2022 at 16:26

1 vote

1 answer

103 views

Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

asked Nov 5, 2022 at 16:33

1 vote

0 answers

16 views

How can I programmatically retrieve all alternative gene names from Wormbase?

asked Mar 12 at 18:50

1 vote

1 answer

57 views

Understanding "Measurement of mRNA abundance using RNA-seq data" by Wagner et al 2012

asked Jun 12, 2021 at 8:05

0 votes

0 answers

17 views

Does GSEA assume that genes sets must involve genes that are POSITIVELY correlated with each other?

asked Mar 21 at 1:54

0 votes

1 answer

66 views

Extracting all information about a sample when using xtract from e-utilities

asked Aug 6, 2020 at 17:13

0 votes

1 answer

385 views

TopHat2 versus HISAT2 inner workings

asked Sep 12, 2020 at 1:24

0 votes

1 answer

33 views

Sample versus subject in scRNA-seq

asked Jul 31, 2021 at 10:07

0 votes

1 answer

323 views

Limma decideTests function: what kind of multiple hypothesis testing correction does parameter "method" involve?

asked Aug 11, 2021 at 21:30

0 votes

0 answers

14 views

xtract from eutilities not exctracting the information I need

asked Nov 14, 2021 at 0:50

0 votes

0 answers

192 views

Unable to gunzip fastq files from ENA

asked May 17, 2020 at 16:07

Stack Exchange Network

40 Questions

Programmatically retrieve Metadata from SRA Run Selector

Using bioconductor from Python

Why are asymmetric distributions an issue for GSEA?

How can I obtain FTP links to studies in ENA given a BioProject ID?

Advantages of paired-end sequencing compared to single end

GSEA: Computing an Enrichment Score (as described in the original paper)

Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data

Programmatically retrieve Accession List from NCBI

Too many requests error when querying NCBI

What is the best way to get a large number of RNA seq data from SRA in Python without being denied access

Tools for creating gene coexpression networks

Importing a WGCNA co-expression network into a networkX graph in Python

Loading all PPI information from Uniprot into a graph in NetworkX

Weighted Network Analysis Book by Steve Horvath, taking the power of a matrix

How to tell if library generation for RNA-seq experiments are stranded vs not stranded

What is a good rule of thumb for the threshold of noise versus signal for RPK in RNA seq?

Trying to download a large number of files from ENA programmatically

What unit (TPM, FPKM/RPKM, or other) to use when working across samples

Can I use a tool for highly variable gene selection for selecting highly variable "bins" from an ATACSeq dataset?

What does the "filters" argument in "getBM" do?

Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

How can I programmatically retrieve all alternative gene names from Wormbase?

Understanding "Measurement of mRNA abundance using RNA-seq data" by Wagner et al 2012

Does GSEA assume that genes sets must involve genes that are POSITIVELY correlated with each other?

Extracting all information about a sample when using xtract from e-utilities

TopHat2 versus HISAT2 inner workings

Sample versus subject in scRNA-seq

Limma decideTests function: what kind of multiple hypothesis testing correction does parameter "method" involve?

xtract from eutilities not exctracting the information I need

Unable to gunzip fastq files from ENA