User An Ignorant Wanderer

4 votes

1 answer

567 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

154 views

Why are asymmetric distributions an issue for GSEA?

asked Mar 21 at 2:13

2 votes

1 answer

144 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

2 answers

3k views

Advantages of paired-end sequencing compared to single end

asked Sep 12, 2020 at 15:15

2 votes

1 answer

91 views

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

asked Jul 10, 2021 at 6:48

2 votes

1 answer

168 views

Programmatically retrieve Accession List from NCBI

asked Jul 8, 2020 at 22:46

2 votes

4 answers

542 views

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

asked Jul 12, 2020 at 23:03

1 vote

1 answer

47 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

2 answers

342 views

Too many requests error when querying NCBI

asked Jul 9, 2020 at 21:25

1 vote

1 answer

289 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

0 answers

197 views

Trying to download a large number of files from ENA programmatically

asked Jul 12, 2020 at 18:17

1 vote

2 answers

293 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

58 views

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

asked Jun 12, 2021 at 8:05

1 vote

1 answer

712 views

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

asked Jun 7, 2020 at 1:48

1 vote

2 answers

419 views

Tools for creating gene coexpression networks

asked May 11, 2020 at 20:59

1 vote

1 answer

283 views

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

asked May 12, 2020 at 19:01

1 vote

1 answer

137 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

1 answer

55 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

94 views

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

asked Nov 5, 2022 at 16:26

1 vote

1 answer

162 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

17 views

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

asked Mar 12 at 18:50

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

0 answers

200 views

Unable to gunzip fastq files from ENA

asked May 17, 2020 at 16:07

0 votes

1 answer

51 views

Programmatically retrieve graph features from Cytoscape

asked Apr 18, 2020 at 4:44

0 votes

2 answers

319 views

Difference between PPI networks and Gene Co-expression networks

asked May 7, 2020 at 15:20

0 votes

1 answer

185 views

Speeding up network creation in WGCNA

asked May 16, 2020 at 18:17

0 votes

2 answers

79 views

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

asked Jun 9, 2020 at 2:32

0 votes

4 answers

229 views

Files for paired end RNA sequencing

asked Jun 9, 2020 at 14:50

Stack Exchange Network

40 Questions

Programmatically retrieve Metadata from SRA Run Selector

Using bioconductor from Python

Why are asymmetric distributions an issue for GSEA?

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

Advantages of paired-end sequencing compared to single end

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

Programmatically retrieve Accession List from NCBI

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

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

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

Trying to download a large number of files from ENA programmatically

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

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

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

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

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?

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

Unable to gunzip fastq files from ENA

Programmatically retrieve graph features from Cytoscape

Difference between PPI networks and Gene Co-expression networks

Speeding up network creation in WGCNA

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

Files for paired end RNA sequencing