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353 results • Page 2 of 8
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45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 16 days ago by 38k • written 4.6 years ago by 84k
0
votes
0
replies
754
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
21 months ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
967
views
Tutorial: Slurm and parallelization
slurm
21 months ago by Juke34 7.8k
1
vote
0
replies
939
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
22 months ago by Pratik ▴ 880
12
votes
1
reply
2.0k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 22 months ago by ★ 14k • written 22 months ago by 84k
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 16 days ago by 38k • written 4.7 years ago by 70k
4
votes
0
replies
907
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
22 months ago by pbpanigrahi ▴ 420
0
votes
1
reply
753
views
Tutorial: Add Customized Filters in GDC
gdc
updated 22 months ago by 21k • written 22 months ago by ▴ 750
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 15 days ago by 38k • written 3.8 years ago by ★ 14k
4
votes
2
replies
2.0k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 15 days ago by 38k • written 3.8 years ago by ★ 9.3k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 690
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 15 days ago by 38k • written 2.6 years ago by ▴ 140
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 15 days ago by 38k • written 6.7 years ago by 26k
21
votes
2
replies
3.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 6 months ago by ▴ 40 • written 23 months ago by 7.8k
31
votes
6
replies
8.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 15 days ago by 38k • written 2.9 years ago by 84k
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 months ago by • 0 • written 9.5 years ago by ★ 7.7k
8
votes
0
replies
2.1k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
2.0 years ago by rpolicastro 11k
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.7 years ago by ★ 4.6k
6
votes
0
replies
1.5k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
2.0 years ago by rpolicastro 11k
8
votes
1
reply
1.0k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 15 days ago by 38k • written 2.0 years ago by 84k
20
votes
10
replies
4.7k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 15 days ago by 38k • written 2.6 years ago by 11k
12
votes
2
replies
1.0k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 15 days ago by 38k • written 2.0 years ago by 11k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 1.6k
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 15 days ago by 38k • written 2.5 years ago by 2.9k
4
votes
0
replies
1.7k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 15 days ago by 38k • written 2.9 years ago by 70k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 15 days ago by 38k • written 3.8 years ago by ▴ 310
275
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 29 days ago by 38k • written 9.4 years ago by 20k
5
votes
0
replies
3.5k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 15 days ago by 38k • written 2.2 years ago by 127k
10
votes
0
replies
4.5k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 15 days ago by 38k • written 2.2 years ago by 127k
10
votes
0
replies
2.7k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 15 days ago by 38k • written 2.2 years ago by 127k
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 15 days ago by 38k • written 2.2 years ago by ★ 23k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 23 days ago by 38k • written 9.0 years ago by ★ 1.9k
0
votes
1
reply
2.4k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 15 days ago by 38k • written 4.6 years ago by ▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 17 months ago by 38k • written 8.8 years ago by 19k
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 15 days ago by 38k • written 5.1 years ago by ▴ 340
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 27 days ago by 38k • written 9.2 years ago by 5.9k
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 days ago by • 0 • written 5.4 years ago by ▴ 130
16
votes
11
replies
7.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
15 days ago by Ram 38k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
15 days ago by Ram 38k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 15 days ago by 38k • written 4.6 years ago by 16k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 15 days ago by 38k • written 6.8 years ago by ▴ 170
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 15 days ago by 38k • written 3.6 years ago by 70k
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 300
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 15 days ago by 38k • written 3.5 years ago by 19k
10
votes
1
reply
2.0k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 15 days ago by 38k • written 3.0 years ago by ★ 2.4k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 15 days ago by 38k • written 6.5 years ago by ★ 3.3k
11
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 15 days ago by 38k • written 2.5 years ago by 84k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 15 days ago by 38k • written 3.3 years ago by 7.8k
353 results • Page 2 of 8
Recent Votes
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR
STARsolo config for 10x Chromium v1, v2, v3
Answer: How to remove unknown batch-batch effects from GEO datasets
Any tips in landing a bioinformatic job?
A: correlation between SCRNA-Seq and bulk RNAseq
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Recent Replies
Answer: Convert .bam file from version 1.6 to 1.4 by Istvan Albert 97k
I think that if you should be able to convert you BAM file to SAM with the current version of `samtools`, then you use an older version of …
Answer: ChIPseeker Warning Message by ATpoint 70k
That happens when you merge or compare GRanges objects that have different chromosomes in it. Either your input or the content from org.Mm.…
Comment: extract gene coordinates and TSS from gene list by Chironex ▴ 40
thank you, I was able to get the coordinates of the gene, but I need to extract the TSS and extend it to 1000 bp.
Answer: extract gene coordinates and TSS from gene list by Carlo Yague 8.3k
I'm not going to give you a complete answer, but you can start looking at this posts: https://www.biostars.org/p/147351/ And use the [R …
Comment: How to make "Custom annotation File" for GO analysis using TOPgo by Shred ★ 1.1k
Do not post screenshots: instead use some lines of input and the desired output.
Comment: Snakemake doesn't recognize output files even though they are created by Shred ★ 1.1k
Sorry but I'm not able to properly understand your scenario. Did your pipeline complete the dry run?
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
Thank you very much for your response.
Answer: How to remove unknown batch-batch effects from GEO datasets by Gordon Smyth ★ 5.6k
removeBatchEffect() wouldn't produce the outlier effect that you show on the right unless there was something seriously wrong with the batc…
Answer: How to get subset of a Seurat object based on metadata? by fracarb8 ▴ 940
To keep the subset call as clean as possible, you can: Idents(skin) <- "predicted_cell_type" cell_values <- c("0:CD8 T cell") …
Answer: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
R codes： library(tidyverse) ####数据获取#### #引文 #citation(package = "GEOquery") #数据提取 GSE53625_matrix<-GEOquery::getGEO(GEO = "GSE5362…
Answer: Any tips in landing a bioinformatic job? by iraun 5.9k
Hi Jorge! In addition to what has already been said, I found my first bioinformatics job in Spain (Barcelona), using this webpage: [http…
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
It is a great honor to receive your response. The data in question is sourced from GSE53625. While using arrayQualityMetrics to assess the…
Answer: Extract data from Signac RegionMatrix? by Chironex ▴ 40
object@assays$ATAC@positionEnrichment$my_region_matrix and also object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job? by ATpoint 70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets by ATpoint 70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
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