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353 results • Page
1 of 8
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Votes
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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
Ram
38k • written 7.7 years ago by
TriS
★ 4.6k
130
votes
123
replies
29k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 7 days ago by
krushnach80
★ 1.1k • written 4.4 years ago by
Kevin Blighe
84k
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
Ram
38k • written 4.6 years ago by
Kevin Blighe
84k
75
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 15 days ago by
Ram
38k • written 5.1 years ago by
Kevin Blighe
84k
144
votes
68
replies
43k
views
18 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 16 days ago by
Ram
38k • written 5.4 years ago by
Kevin Blighe
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
Ram
38k • written 4.7 years ago by
ATpoint
70k
72
votes
60
replies
23k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 6 weeks ago by
Ram
38k • written 5.6 years ago by
Kevin Blighe
84k
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
Ram
38k • written 6.5 years ago by
steve
★ 3.3k
72
votes
48
replies
15k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 4 weeks ago by
Ram
38k • written 10.1 years ago by
lh3
33k
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
59
votes
43
replies
18k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 15 days ago by
Ram
38k • written 5.5 years ago by
Rox
★ 1.4k
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
Acadia
• 0 • written 9.4 years ago by
Irsan
★ 7.7k
17
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
Ram
38k • written 6.8 years ago by
Esaie
▴ 160
276
votes
39
replies
164k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 5 days ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
146
votes
35
replies
58k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 4 weeks ago by
Ram
38k • written 10.3 years ago by
vijay
★ 1.6k
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork
enrichment
pathway
R
updated 20 days ago by
Ram
38k • written 4.8 years ago by
egeulgen
★ 1.3k
145
votes
34
replies
51k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 4 weeks ago by
Ram
38k • written 10.0 years ago by
Cyriac Kandoth
5.9k
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
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
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
12
votes
31
replies
4.7k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 20 days ago by
Ram
38k • written 3.6 years ago by
Juke34
7.8k
82
votes
28
replies
28k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 6 weeks ago by
Ram
38k • written 7.1 years ago by
Obi Griffith
20k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 27 days ago by
Ram
38k • written 9.1 years ago by
Istvan Albert
97k
64
votes
26
replies
11k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 15 days ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
84k
64
votes
26
replies
11k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 16 days ago by
Ram
38k • written 4.1 years ago by
finswimmer
16k
136
votes
25
replies
75k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 11 months ago by
Ram
38k • written 10.9 years ago by
Ying W
★ 4.2k
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 5 weeks ago by
Ram
38k • written 10.5 years ago by
Istvan Albert
97k
58
votes
25
replies
36k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 12 days ago by
Ram
38k • written 6.7 years ago by
Shicheng Guo
★ 9.3k
9
votes
23
replies
8.3k
views
7 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
orthomcl
ubuntu
linux
mysql
Tutorial
4.8 years ago by
vimalkvn
▴ 310
18
votes
22
replies
7.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 15 days ago by
Ram
38k • written 3.3 years ago by
Juke34
7.8k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 10 months ago by
Ram
38k • written 8.3 years ago by
Parham
★ 1.6k
82
votes
21
replies
15k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 20 days ago by
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
2.9k
82
votes
21
replies
71k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 5 weeks ago by
cmdcolin
★ 2.9k • written 4.7 years ago by
otwtgin2010
▴ 540
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
Ram
38k • written 3.8 years ago by
jared.andrews07
★ 14k
51
votes
19
replies
41k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 5 weeks ago by
Ram
38k • written 11.0 years ago by
Sukhi Singh
11k
23
votes
19
replies
5.7k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
mutation
fastq
cancer
target
Tutorial
updated 5.2 years ago by
lebedana21
• 0 • written 6.5 years ago by
chen
★ 2.4k
89
votes
19
replies
30k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 28 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
42
votes
19
replies
7.1k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 4 weeks ago by
Ram
38k • written 10.1 years ago by
Daniel Standage
4.1k
8
votes
19
replies
12k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 20 days ago by
Ram
38k • written 8.4 years ago by
Lesley Sitter
▴ 580
47
votes
19
replies
12k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 11 weeks ago by
Ram
38k • written 10.1 years ago by
Istvan Albert
97k
8
votes
17
replies
2.3k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
alignment
next-gen-sequencing
RNA-seq
updated 7 months ago by
Ram
38k • written 7.5 years ago by
elia.brodsky
▴ 340
26
votes
17
replies
6.7k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 6 months ago by
Ram
38k • written 8.6 years ago by
Ian
5.9k
12
votes
17
replies
2.2k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 3 months ago by
Ram
38k • written 7.8 years ago by
Istvan Albert
97k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 15 days ago by
Ram
38k • written 6.6 years ago by
Jean-Karim Heriche
26k
33
votes
16
replies
15k
views
10 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 28 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
42
votes
16
replies
21k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 7 months ago by
Ram
38k • written 7.5 years ago by
Chirag Nepal
★ 2.3k
24
votes
15
replies
7.9k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 4 weeks ago by
Ram
38k • written 10.2 years ago by
Medhat
9.5k
34
votes
15
replies
5.0k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 15 days ago by
Ram
38k • written 3.8 years ago by
Shicheng Guo
★ 9.3k
59
votes
15
replies
11k
views
Tutorial:
Which human reference genome should I use?
genome
alignment
assembly
Tutorial
4.4 years ago by
finswimmer
16k
34
votes
15
replies
18k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 14 days ago by
Ram
38k • written 6.5 years ago by
martinguerrerog89
▴ 310
30
votes
14
replies
15k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 4 weeks ago by
Ram
38k • written 10.2 years ago by
Cyriac Kandoth
5.9k
353 results • Page
1 of 8
Recent Votes
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
Answer: Somatic truth set
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Popular Question
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Bogdan
★ 1.3k
Popular Question
to
pavelasquezv
▴ 50
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to
Anand Rao
▴ 550
Scholar
to
andres.firrincieli
3.2k
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chaco001
▴ 10
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to
Jaykumar
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Recent Replies
Answer: Align miRNA library (small RNA-seq) without trimming
by
Ming Tommy Tang
★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression
by
afei
• 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
by
rebeliscu
▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
by
cfos4698
▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking
by
Mensur Dlakic
★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error
by
Declan
• 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set
by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis
by
Jeremy
▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
by
Carambakaracho
★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
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