Limit : this year
all time today this week this month this year
91 results • Page 2 of 2
Sort: Rank
Rank Views Votes Replies
0
votes
0
replies
703
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
9 months ago by Ming Tommy Tang ★ 3.9k
14
votes
3
replies
20k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 9 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
8
votes
2
replies
1.2k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 9 months ago by 44k • written 9 months ago by ★ 2.5k
1
vote
0
replies
566
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
10
votes
4
replies
5.8k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
9 months ago by Hamid Ghaedi 3.2k
7
votes
0
replies
619
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.2k
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
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
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 10 months ago by • 0 • written 8.2 years ago by 20k
1
vote
0
replies
708
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 10 months ago by 44k • written 10 months ago by ★ 3.9k
23
votes
13
replies
11k
views
11 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 6 months ago by • 0 • written 23 months ago by 82k
2
votes
0
replies
3.2k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 10 months ago by 44k • written 10 months ago by ★ 3.9k
19
votes
7
replies
6.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 months ago by 82k • written 4.2 years ago by 6.4k
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
10 months ago by Ming Tommy Tang ★ 3.9k
93
votes
23
replies
93k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.8 years ago by ▴ 610
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
4
votes
0
replies
797
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
11 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
712
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 11 months ago by 44k • written 11 months ago by ★ 3.9k
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
1
vote
2
replies
914
views
Tutorial: How to ask computational biology questions
computational-biology
updated 11 months ago by 44k • written 11 months ago by ★ 3.9k
1
vote
0
replies
705
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 11 months ago by 44k • written 11 months ago by ★ 3.9k
3
votes
0
replies
769
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
11 months ago by Ming Tommy Tang ★ 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
0
votes
0
replies
710
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
11 months ago by Coremine Medical ▴ 20
2
votes
0
replies
741
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 11 months ago by 44k • written 11 months ago by ▴ 20
1
vote
0
replies
846
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 6 months ago by 44k • written 14 months ago by ▴ 10
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 6 months ago by • 0 • written 16 months ago by ★ 1.6k
2
votes
0
replies
1.3k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 11 months ago by 44k • written 17 months ago by ▴ 420
1
vote
0
replies
2.7k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 11 months ago by 44k • written 17 months ago by ▴ 420
5
votes
0
replies
1.7k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 11 months ago by 44k • written 17 months ago by ▴ 420
1
vote
2
replies
1.6k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 11 months ago by 44k • written 20 months ago by ▴ 20
83
votes
34
replies
19k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 12 months ago by • 0 • written 5.9 years ago by ★ 1.3k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 11 months ago by 44k • written 5.3 years ago by ▴ 170
150
votes
70
replies
51k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 months ago by ▴ 260 • written 6.5 years ago by 88k
3
votes
1
reply
3.5k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 3 months ago by ▴ 120 • written 2.8 years ago by 88k
102
votes
106
replies
47k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 weeks ago by ▴ 20 • written 5.7 years ago by 88k
6
votes
2
replies
5.1k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by GenoMax 142k
21
votes
26
replies
9.8k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 10 weeks ago by ▴ 30 • written 4.5 years ago by 8.6k
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by • 0 • written 10.3 years ago by 100k
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 11 months ago by 44k • written 6.6 years ago by ★ 2.5k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 8 months ago by ▴ 20 • written 8.9 years ago by ▴ 430
91 results • Page 2 of 2
Recent Votes
DESeq2 single cell pseudobulk
Comment: Number of non-ATCG nucleotides replaced by Salmon
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: Error when i use EVidenceModeler to do the genome annotation
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
Recent Locations • All
Karolinska Institutet, Sweden, 4 minutes ago
Cambridge, MA, 9 minutes ago
Austria, 12 minutes ago
Sweden, 14 minutes ago
Belgium, 18 minutes ago
Taiwan, 34 minutes ago
USA, 36 minutes ago
Recent Awards • All
Teacher to Rob 6.6k
Popular Question to seta ★ 1.9k
Popular Question to melissachua90 ▴ 70
Popular Question to Hamtaro ▴ 50
Popular Question to ericrkofman ▴ 20
Scholar to chrchang523 10k
Popular Question to garcesj ▴ 50
Recent Replies
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…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files by Deepthi • 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
Comment: Mutation counts corrected by number of samples by Ram 44k
> I want to compare the number of mutations This comparison will give you literally no useful information.
Traffic: 1605 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