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124 results • Page 1 of 3
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239
votes
176
replies
96k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 months ago by 43k • written 8.8 years ago by ★ 4.7k
150
votes
70
replies
51k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 8 months ago by ▴ 260 • written 6.5 years ago by 88k
100
votes
106
replies
47k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 5 weeks ago by ▴ 20 • written 5.7 years ago by 88k
93
votes
23
replies
93k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by • 0 • written 5.8 years ago by ▴ 610
90
votes
48
replies
34k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 6 months ago by 43k • written 10.6 years ago by ★ 7.8k
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 27 days ago by • 0 • written 3.6 years ago by 3.2k
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 months ago by • 0 • written 8.2 years ago by 20k
83
votes
34
replies
19k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 months ago by • 0 • written 5.9 years ago by ★ 1.3k
76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
20 days ago by Kevin Blighe 88k
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
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
65
votes
15
replies
15k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 11 months ago by 43k • written 5.6 years ago by 16k
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 6 weeks ago by 100k • written 8.2 years ago by 43k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 9 weeks ago by • 0 • written 3.6 years ago by 3.2k
39
votes
16
replies
37k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 months ago by 142k • written 3.8 years ago by ▴ 160
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 8.8 years ago by ▴ 430
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 weeks ago by ▴ 30 • written 7.6 years ago by ▴ 310
21
votes
13
replies
11k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 6 months ago by • 0 • written 22 months ago by 82k
21
votes
26
replies
9.7k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 8 weeks ago by ▴ 30 • written 4.4 years ago by 8.6k
20
votes
2
replies
8.1k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.4k
19
votes
7
replies
6.6k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 months ago by 82k • written 4.1 years ago by 6.4k
15
votes
1
reply
7.2k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.0k
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
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 12 months ago by 43k • written 3.2 years ago by ▴ 420
10
votes
1
reply
9.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 12 months ago by 43k • written 6.7 years ago by ▴ 110
10
votes
4
replies
5.7k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
9 months ago by Hamid Ghaedi 3.2k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 7 weeks ago by 43k • written 6.2 years ago by 88k
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.3 years ago by ▴ 320
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 12 months ago by 43k • written 6.7 years ago by 88k
8
votes
2
replies
1.2k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 9 months ago by 43k • written 9 months ago by ★ 2.5k
7
votes
3
replies
3.0k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 26 days ago by 6.4k • written 16 months ago by ▴ 130
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 11 months ago by 43k • written 5.2 years ago by ▴ 170
7
votes
0
replies
609
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.1k
7
votes
1
reply
185
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 8 days ago by 14k • written 8 days ago by ▴ 360
7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 12 months ago by 43k • written 6.6 years ago by ★ 1.7k
6
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ▴ 140
6
votes
1
reply
477
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
6
votes
2
replies
5.0k
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
6
votes
0
replies
578
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
5
votes
5
replies
655
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 12 days ago by • 0 • written 20 days ago by ★ 3.9k
5
votes
13
replies
1.9k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 25 days ago by 82k • written 26 days ago by ★ 1.7k
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 43k • written 16 months ago by ▴ 420
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 12 months ago by 43k • written 6.7 years ago by 35k
4
votes
0
replies
787
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
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
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
3
votes
1
reply
3.4k
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
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
3
votes
1
reply
654
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.6k
3
votes
4
replies
3.6k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 11 months ago by 43k • written 5.5 years ago by ▴ 340
124 results • Page 1 of 3
Recent Votes
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
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Recent Replies
Comment: Filtering VCF files based on VAF giving incorrect results by Arton • 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R by Ghada • 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome by Zhenyu Zhang ★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R by marco.barr ▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome by shpak.max ▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Pierre Lindenbaum 161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome by Pierre Lindenbaum 161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline? by yura.grabovska ▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file by asalimih ▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R by Lélé ▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations by GenoMax 142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations by Pierre Lindenbaum 161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R by Ghada • 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R by jared.andrews07 ★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
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