User Peter

18 votes

2 answers

3k views

How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq?

rna-seq sequencing

asked Jun 13, 2017 at 13:03

16 votes

4 answers

2k views

Why Bioconductor?

r bioconductor

asked Jun 11, 2017 at 1:28

13 votes

4 answers

3k views

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

rna-seq r

asked Jun 13, 2017 at 10:23

9 votes

3 answers

3k views

Convert R RNA-seq data object to a Python object

rna-seq r python

asked Mar 21, 2018 at 16:27

9 votes

4 answers

971 views

Ultimate reproducibility in R?

r reproducibility workflow-management

asked Aug 31, 2017 at 14:06

8 votes

7 answers

1k views

What are the available cloud computing services for bioinformatics? [closed]

linux

asked Jun 12, 2017 at 11:51

8 votes

3 answers

486 views

What are the ways to keep track of branches in the analysis?

r bioconductor git workflow-management best-practice

asked Jun 15, 2017 at 11:13

7 votes

3 answers

4k views

Retrieve detailed gene descriptions

r gene annotation public-databases

asked Oct 14, 2017 at 16:31

7 votes

1 answer

130 views

Network comparison of single cells (from sequencing data)

rna-seq scrnaseq networks single-cell

asked May 29, 2018 at 13:50

5 votes

3 answers

200 views

Show presence of known mutation in RNA-seq data

rna-seq alignment snp rna-alignment mutations

asked Dec 18, 2017 at 16:31

5 votes

4 answers

2k views

Pathway level analysis of single-cell gene expression

r scrnaseq pathway

asked May 23, 2018 at 16:03

5 votes

1 answer

77 views

Should the cell sorting marker genes be excluded during clustering?

rna-seq cell-line clustering

asked Jun 13, 2017 at 16:02

5 votes

1 answer

724 views

What are the ways to process a list of differentially expressed genes?

rna-seq r deseq2 networks

asked Jun 8, 2017 at 12:07

4 votes

1 answer

2k views

10x Genomics Chromium single-cell RNA-seq data analysis options?

rna-seq r bioconductor scrnaseq 10x-genomics

asked Jun 16, 2017 at 11:22

3 votes

2 answers

3k views

Handling sample identity in aggregated 10x libraries?

rna-seq r scrnaseq 10x-genomics

asked Jun 16, 2017 at 12:17

3 votes

3 answers

1k views

Receptor-ligand database

database public-databases protein-protein-interaction

asked Oct 22, 2018 at 11:05

2 votes

1 answer

62 views

Sequence alignment of extended IUPAC sequences

sequence-alignment

asked Mar 2, 2020 at 11:33

2 votes

1 answer

111 views

Create identicon of a DNA sequence

visualization egf

asked Nov 28, 2020 at 13:06

2 votes

1 answer

3k views

Cellranger aggr and Seurat merge difference?

rna-seq single-cell

asked Aug 22, 2017 at 10:11

2 votes

1 answer

88 views

Obtain CD (cluster of differentiation) marker expression information

r annotation gene-ontology flow-cytometry

asked Oct 17, 2017 at 16:42

2 votes

1 answer

295 views

Mini-bulk RNA-seq and scRNA-seq analysis differences?

rna-seq sequence-analysis single-cell

asked Dec 6, 2017 at 10:56

1 vote

1 answer

42 views

Convert sequence in MS doc to fasta or genbank

fasta format-conversion genbank egf

asked Nov 23, 2020 at 16:41

1 vote

1 answer

173 views

List of human transcription factors

database data-retrieval human

asked Nov 5, 2018 at 15:00

1 vote

2 answers

989 views

Find a cutoff value for genes that are expressed in single cell RNA-seq?

rna-seq scrnaseq gene-expression

asked Sep 17, 2018 at 14:34

0 votes

2 answers

198 views

Visualize network (graph) using "line" layout

networks visualization

asked Sep 10, 2018 at 16:35

0 votes

1 answer

62 views

Calculating celltype proportion changes between conditions in single-cell data

scrnaseq single-cell

asked Nov 20, 2019 at 18:06

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26 Questions

How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq?

Why Bioconductor?

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

Convert R RNA-seq data object to a Python object

Ultimate reproducibility in R?

What are the available cloud computing services for bioinformatics? [closed]

What are the ways to keep track of branches in the analysis?

Retrieve detailed gene descriptions

Network comparison of single cells (from sequencing data)

Show presence of known mutation in RNA-seq data

Pathway level analysis of single-cell gene expression

Should the cell sorting marker genes be excluded during clustering?

What are the ways to process a list of differentially expressed genes?

10x Genomics Chromium single-cell RNA-seq data analysis options?

Handling sample identity in aggregated 10x libraries?

Receptor-ligand database

Sequence alignment of extended IUPAC sequences

Create identicon of a DNA sequence

Cellranger aggr and Seurat merge difference?

Obtain CD (cluster of differentiation) marker expression information

Mini-bulk RNA-seq and scRNA-seq analysis differences?

Convert sequence in MS doc to fasta or genbank

List of human transcription factors

Find a cutoff value for genes that are expressed in single cell RNA-seq?

Visualize network (graph) using "line" layout

Calculating celltype proportion changes between conditions in single-cell data