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142 results • Page
1 of 3
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Votes
Replies
239
votes
176
replies
95k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 15 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
93
votes
23
replies
92k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
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
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
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
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
76
votes
71
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 2 days ago by
GenoMax
141k • written 6.2 years ago by
Kevin Blighe
87k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by
snardeli
• 0 • written 10.2 years ago by
Istvan Albert
100k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 5 weeks ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
65
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 11 months ago by
Ram
43k • written 5.5 years ago by
finswimmer
16k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 27 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 6 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 11 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 11 months ago by
GenoMax
141k • written 10.4 years ago by
Obi Griffith
20k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 5 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 5 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
21
votes
13
replies
10k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 5 months ago by
jude
• 0 • written 22 months ago by
ATpoint
82k
20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 11 months ago by
Ram
43k • written 7.0 years ago by
support
▴ 650
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 11 months ago by
Ram
43k • written 6.4 years ago by
bernatgel
★ 3.4k
19
votes
7
replies
6.5k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 9 months ago by
ATpoint
82k • written 4.1 years ago by
colindaven
6.4k
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Sej Modha
5.3k
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Michael
54k
15
votes
1
reply
7.1k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 11 months ago by
Ram
43k • written 6.4 years ago by
Joseph Hughes
★ 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 8 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
12
votes
11
replies
7.5k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 11 months ago by
Ram
43k • written 7.1 years ago by
CandiceChuDVM
★ 2.4k
11
votes
7
replies
14k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
11
votes
7
replies
11k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 11 months ago by
Ram
43k • written 3.1 years ago by
Novogene
▴ 420
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 28 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
10
votes
2
replies
3.7k
views
Tutorial:
Graph visualization with igraph in R
Visualization
igraph
Graph
R
Network
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Jean-Karim Heriche
27k
10
votes
1
reply
9.2k
views
Tutorial:
How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 6.6 years ago by
imlituan
▴ 110
9
votes
4
replies
5.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
9
votes
5
replies
2.3k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
8
votes
2
replies
1.1k
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 8 months ago by
Ram
43k • written 8 months ago by
carlopecoraro2
★ 2.5k
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 10 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
7
votes
2
replies
1.9k
views
Tutorial:
Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by
Ram
43k • written 6.7 years ago by
bdolin
▴ 90
7
votes
0
replies
590
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
7
votes
1
reply
2.2k
views
Tutorial:
A gentle introduction to biogo
sequence
golang
biogo
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Botond Sipos
★ 1.7k
6
votes
0
replies
526
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 11 weeks ago by
zx8754
11k • written 11 weeks ago by
Ming Tommy Tang
★ 3.9k
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
4 months ago by
GenoMax
141k
6
votes
2
replies
4.2k
views
Tutorial:
GATK method for filtering vcf lines using GT values at all or multisample level.
genome
vcf
genotype
variant-filtration
updated 11 months ago by
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
6
votes
1
reply
428
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 130
5
votes
0
replies
1.6k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates
by
Sofia
• 0
Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt
by
Greg
• 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
Comment: PCA plot (Suggestions Needed)
by
jkim
▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
mropri
▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
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