User Peter

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

rna-seq sequencing

May 12 '19 at 11:00 M__ 5,583

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16

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4

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Why Bioconductor?

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

rna-seq r

Jun 15 '17 at 9:53 Ian Sudbery 3,061

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8

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3

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Convert R RNA-seq data object to a Python object

rna-seq r python

Sep 4 at 11:17 Dr_Hope 243

1

8

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4

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849

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Ultimate reproducibility in R?

r reproducibility workflow-management

Sep 12 '17 at 9:12 agapow 748

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7

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1k

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

linux

Aug 15 '17 at 17:50 Community♦ 1

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8

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3

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438

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

r bioconductor git workflow-management best-practice

Jun 15 '17 at 15:57 Konrad Rudolph 4,505

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93

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Network comparison of single cells (from sequencing data)

rna-seq scrnaseq networks single-cell

May 30 '18 at 12:33 llrs 4,480

6

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3

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3k

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Retrieve detailed gene descriptions

r gene annotation public-databases

Aug 14 '19 at 11:27 flying sheep 121

1

5

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4

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2k

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Pathway level analysis of single-cell gene expression

r scrnaseq pathway

Sep 3 at 15:34 mfalco 1

5

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3

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169

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Show presence of known mutation in RNA-seq data

rna-seq alignment snp rna-alignment mutations

Sep 8 '19 at 18:29 Peter 2,497

5

votes

1

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70

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Should the cell sorting marker genes be excluded during clustering?

rna-seq cell-line clustering

Jun 14 '17 at 16:34 olga 481

1

5

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1

answer

640

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

rna-seq r deseq2 networks

Jun 8 '17 at 14:37 gringer 9,873

4

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1

answer

2k

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

rna-seq r bioconductor scrnaseq 10x-genomics

Jun 16 '17 at 14:26 Peter 2,497

3

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3

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1k

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Receptor-ligand database

database public-databases protein-protein-interaction

Dec 9 at 2:23 Tapper 65

3

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2

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2k

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Handling sample identity in aggregated 10x libraries?

rna-seq r scrnaseq 10x-genomics

Jun 14 '18 at 21:48 jia 1

2

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1

answer

98

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Create identicon of a DNA sequence

visualization egf

Nov 28 at 13:06 Peter 2,497

2

votes

1

answer

46

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Sequence alignment of extended IUPAC sequences

sequence-alignment

Mar 4 '20 at 9:24 StupidWolf 1,613

2

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1

answer

205

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

rna-seq sequence-analysis single-cell

Dec 13 '17 at 18:51 burger 2,037

2

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1

answer

75

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Obtain CD (cluster of differentiation) marker expression information

r annotation gene-ontology flow-cytometry

Oct 18 '17 at 6:33 neilfws 636

1

2

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1

answer

2k

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Cellranger aggr and Seurat merge difference?

rna-seq single-cell

Aug 24 '17 at 0:15 burger 2,037

1

vote

1

answer

21

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Convert sequence in MS doc to fasta or genbank

fasta format-conversion genbank egf

Nov 23 at 16:41 Peter 2,497

1

vote

1

answer

147

views

List of human transcription factors

database data-retrieval human

Nov 5 '18 at 16:44 llrs 4,480

1

vote

2

answers

559

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

rna-seq scrnaseq gene-expression

Oct 26 '18 at 6:25 BC Wang 17

1

0

votes

1

answer

22

views

Calculating celltype proportion changes between conditions in single-cell data

scrnaseq single-cell

Nov 20 '19 at 18:15 Peter 2,497

0

votes

1

answer

135

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Visualize network (graph) using “line” layout

networks visualization

Sep 12 '18 at 7:36 llrs 4,480

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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?

Network comparison of single cells (from sequencing data)

Retrieve detailed gene descriptions

Pathway level analysis of single-cell gene expression

Show presence of known mutation in RNA-seq data

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?

Receptor-ligand database

Handling sample identity in aggregated 10x libraries?

Create identicon of a DNA sequence

Sequence alignment of extended IUPAC sequences

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

Obtain CD (cluster of differentiation) marker expression information

Cellranger aggr and Seurat merge difference?

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?

Calculating celltype proportion changes between conditions in single-cell data

Visualize network (graph) using “line” layout