An Ignorant Wanderer's user avatar
An Ignorant Wanderer's user avatar
An Ignorant Wanderer's user avatar
An Ignorant Wanderer
  • Member for 3 years, 8 months
  • Last seen more than a month ago
4 votes
1 answer
567 views

Programmatically retrieve Metadata from SRA Run Selector

3 votes
3 answers
3k views

Using bioconductor from Python

3 votes
1 answer
154 views

Why are asymmetric distributions an issue for GSEA?

2 votes
1 answer
144 views

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

2 votes
2 answers
3k views

Advantages of paired-end sequencing compared to single end

2 votes
1 answer
91 views

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

2 votes
1 answer
168 views

Programmatically retrieve Accession List from NCBI

2 votes
4 answers
542 views

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

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?

1 vote
2 answers
342 views

Too many requests error when querying NCBI

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

1 vote
0 answers
197 views

Trying to download a large number of files from ENA programmatically

1 vote
2 answers
293 views

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

1 vote
1 answer
58 views

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

1 vote
1 answer
712 views

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

1 vote
2 answers
419 views

Tools for creating gene coexpression networks

1 vote
1 answer
283 views

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

1 vote
1 answer
137 views

Loading all PPI information from Uniprot into a graph in NetworkX

1 vote
1 answer
43 views

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

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?

1 vote
1 answer
94 views

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

1 vote
1 answer
162 views

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

1 vote
0 answers
17 views

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

0 votes
0 answers
17 views

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

0 votes
0 answers
200 views

Unable to gunzip fastq files from ENA

0 votes
1 answer
51 views

Programmatically retrieve graph features from Cytoscape

0 votes
2 answers
319 views

Difference between PPI networks and Gene Co-expression networks

0 votes
1 answer
185 views

Speeding up network creation in WGCNA

0 votes
2 answers
79 views

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

0 votes
4 answers
229 views

Files for paired end RNA sequencing