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231 results • Page
1 of 5
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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 10 days ago by
krushnach80
★ 1.1k • written 4.5 years ago by
Kevin Blighe
85k
92
votes
105
replies
34k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 18 days ago by
Ram
38k • written 4.6 years ago by
Kevin Blighe
85k
75
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 17 days ago by
Ram
38k • written 5.1 years ago by
Kevin Blighe
85k
144
votes
69
replies
43k
views
19 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 1 day ago by
k001
▴ 10 • written 5.4 years ago by
Kevin Blighe
85k
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 18 days ago by
Ram
38k • written 4.7 years ago by
ATpoint
71k
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 7 weeks ago by
Ram
38k • written 5.6 years ago by
Kevin Blighe
85k
60
votes
52
replies
39k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 17 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 5 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 17 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 9.5 years ago by
Irsan
★ 7.7k
18
votes
40
replies
16k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 17 days ago by
Ram
38k • written 6.8 years ago by
Esaie
▴ 170
276
votes
39
replies
165k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 7 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 5 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 22 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 5 weeks ago by
Ram
38k • written 10.0 years ago by
Cyriac Kandoth
5.9k
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
17 days ago by
Ram
38k
275
votes
33
replies
92k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 4 weeks ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
12
votes
31
replies
4.8k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 22 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 7 weeks ago by
Ram
38k • written 7.1 years ago by
Obi Griffith
20k
64
votes
26
replies
11k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 18 days ago by
Ram
38k • written 4.1 years ago by
finswimmer
16k
64
votes
26
replies
11k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 17 days ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
85k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 29 days ago by
Ram
38k • written 9.1 years ago by
Istvan Albert
97k
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 14 days ago by
Ram
38k • written 6.7 years ago by
Shicheng Guo
★ 9.3k
136
votes
25
replies
75k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 12 months ago by
Ram
38k • written 10.9 years ago by
Ying W
★ 4.2k
18
votes
22
replies
7.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 17 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 11 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 22 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 6 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 17 days ago by
Ram
38k • written 3.8 years ago by
jared.andrews07
★ 14k
42
votes
19
replies
7.1k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 5 weeks ago by
Ram
38k • written 10.1 years ago by
Daniel Standage
4.1k
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
8
votes
19
replies
12k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 22 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
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 4 weeks ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
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
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
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
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 17 days ago by
Ram
38k • written 6.7 years ago by
Jean-Karim Heriche
26k
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
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 4 weeks ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
24
votes
15
replies
7.9k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 5 weeks ago by
Ram
38k • written 10.2 years ago by
Medhat
9.5k
34
votes
15
replies
5.1k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 17 days ago by
Ram
38k • written 3.8 years ago by
Shicheng Guo
★ 9.3k
34
votes
15
replies
18k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 16 days ago by
Ram
38k • written 6.5 years ago by
martinguerrerog89
▴ 310
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 7 weeks ago by
Ram
38k • written 9.9 years ago by
Medhat
9.5k
7
votes
14
replies
2.1k
views
6 follow
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 months ago by
Angelina_G
• 0 • written 13 months ago by
thehung92phuyen
▴ 30
45
votes
14
replies
59k
views
10 follow
Tutorial:
Using R in Conda
R
updated 17 days ago by
Ram
38k • written 2.7 years ago by
rohitsatyam102
▴ 690
30
votes
14
replies
15k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 5 weeks ago by
Ram
38k • written 10.2 years ago by
Cyriac Kandoth
5.9k
231 results • Page
1 of 5
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Popular Question
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zhou_1228
• 0
Teacher
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GenoMax
127k
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to
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★ 23k
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Recent Replies
Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
by
Daniel
• 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
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