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

Programmatically retrieve Metadata from SRA Run Selector

3 votes
2 answers
4k views

Advantages of paired-end sequencing compared to single end

3 votes
3 answers
4k views

Using bioconductor from Python

3 votes
1 answer
298 views

Why are asymmetric distributions an issue for GSEA?

2 votes
1 answer
156 views

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

2 votes
1 answer
93 views

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

2 votes
1 answer
193 views

Programmatically retrieve Accession List from NCBI

2 votes
4 answers
593 views

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

1 vote
1 answer
48 views

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

1 vote
2 answers
409 views

Too many requests error when querying NCBI

1 vote
1 answer
308 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
203 views

Trying to download a large number of files from ENA programmatically

1 vote
2 answers
323 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
758 views

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

1 vote
2 answers
442 views

Tools for creating gene coexpression networks

1 vote
1 answer
297 views

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

1 vote
1 answer
149 views

Loading all PPI information from Uniprot into a graph in NetworkX

1 vote
1 answer
45 views

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

1 vote
1 answer
57 views

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

1 vote
1 answer
214 views

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

1 vote
1 answer
279 views

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

1 vote
0 answers
22 views

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

0 votes
0 answers
216 views

Unable to gunzip fastq files from ENA

0 votes
1 answer
53 views

Programmatically retrieve graph features from Cytoscape

0 votes
2 answers
337 views

Difference between PPI networks and Gene Co-expression networks

0 votes
1 answer
219 views

Speeding up network creation in WGCNA

0 votes
2 answers
85 views

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

0 votes
4 answers
239 views

Files for paired end RNA sequencing

0 votes
3 answers
162 views

What is a good RNA seq normalization method that allows for across sample comparisons and between transcripts