Limit : this year
all time today this week this month this year
91 results • Page 2 of 2
Sort: Views
Rank Views Votes Replies
1
vote
5
replies
693
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
670
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
11 months ago by sinha.shriprakash ▴ 20
2
votes
3
replies
667
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
3
votes
1
reply
666
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 10 months ago by 44k • written 10 months ago by 8.6k
1
vote
0
replies
655
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 44k • written 9 months ago by ★ 3.9k
1
vote
0
replies
627
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
11 months ago by Ming Tommy Tang ★ 3.9k
7
votes
0
replies
620
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.2k
2
votes
0
replies
603
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 8 months ago by 44k • written 8 months ago by 162k
3
votes
2
replies
601
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by 82k • written 4 months ago by ▴ 120
6
votes
0
replies
596
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by 11k • written 3 months ago by ★ 3.9k
0
votes
1
reply
594
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
1
reply
571
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
1
vote
0
replies
567
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
9 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
563
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
7 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
503
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 870
6
votes
1
reply
499
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
1
reply
497
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
0
replies
493
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 months ago by 44k • written 10 months ago by ★ 3.9k
2
votes
0
replies
455
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
425
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 44k • written 5 months ago by ★ 3.9k
0
votes
0
replies
402
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
6 months ago by rohitsatyam102 ▴ 870
1
vote
1
reply
391
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
390
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
384
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
368
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
368
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
353
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
323
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
1
reply
322
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
321
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
320
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
315
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
304
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
298
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
283
views
Tutorial: How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat single-cell ggplot2
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
275
views
Tutorial: Parsing HMMER output
HMMER
updated 9 weeks ago by 142k • written 9 weeks ago by ▴ 140
0
votes
0
replies
273
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
3
votes
0
replies
258
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
3 months ago by Novogene ▴ 420
2
votes
0
replies
241
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
3 months ago by Novogene ▴ 420
1
vote
0
replies
234
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
5 weeks ago by Novogene ▴ 420
7
votes
1
reply
233
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 18 days ago by 14k • written 18 days ago by ▴ 360
91 results • Page 2 of 2
Recent Votes
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
Recent Locations • All
Egypt, 7 minutes ago
Bologna, 25 minutes ago
USA, 32 minutes ago
Germany, 34 minutes ago
United States, 35 minutes ago
United States, 48 minutes ago
Australia, 50 minutes ago
Recent Awards • All
Popular Question to wonde2000 • 0
Teacher to alanh ▴ 170
Popular Question to Pegasus ▴ 100
Teacher to Rob 6.6k
Popular Question to seta ★ 1.9k
Popular Question to melissachua90 ▴ 70
Popular Question to Hamtaro ▴ 50
Recent Replies
Comment: Merging multiple samples in Seurat by Picasa ▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data by Bastien Hervé 5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq) by ATpoint 82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation by peanut • 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon by Tonya S. ▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon by Rob 6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage by Brian Bushnell 20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage by GenoMax 142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage by Brian Bushnell 20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea by sc_analysis • 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data by Sara ▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Traffic: 1466 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6