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411 results • Page
1 of 9
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Votes
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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 8.8 years ago by
TriS
★ 4.7k
133
votes
123
replies
38k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 13 months ago by
1769mkc
★ 1.2k • written 5.5 years ago by
Kevin Blighe
87k
99
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 22 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
6 days ago by
Kevin Blighe
87k
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
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 13 months ago by
Ram
43k • written 5.8 years ago by
ATpoint
82k
73
votes
60
replies
27k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 14 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
60
votes
52
replies
43k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 13 months ago by
Ram
43k • written 7.6 years ago by
steve
★ 3.5k
72
votes
48
replies
18k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 14 months ago by
Ram
43k • written 11.2 years ago by
lh3
33k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
196
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 15 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Rox
★ 1.4k
18
votes
40
replies
18k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.8 years ago by
krishdb38
• 0 • written 7.8 years ago by
Esaie
▴ 170
287
votes
39
replies
183k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 13 months ago by
Ram
43k • written 9.7 years ago by
Obi Griffith
20k
149
votes
35
replies
62k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 14 months ago by
Ram
43k • written 11.4 years ago by
vijay
★ 1.6k
147
votes
34
replies
55k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 14 months ago by
Ram
43k • written 11.0 years ago by
Cyriac Kandoth
6.0k
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 5.9 years ago by
egeulgen
★ 1.3k
298
votes
33
replies
108k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
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
14
votes
31
replies
6.8k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 13 months ago by
Ram
43k • written 4.7 years ago by
Juke34
8.6k
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 4 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
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
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 6 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
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
64
votes
26
replies
14k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 6 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.6k
58
votes
25
replies
40k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Shicheng Guo
★ 9.4k
139
votes
25
replies
84k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 2.1 years ago by
Ram
43k • written 12.0 years ago by
Ying W
★ 4.2k
95
votes
25
replies
33k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 14 months ago by
Ram
43k • written 11.6 years ago by
Istvan Albert
100k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 13 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
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
142
votes
21
replies
30k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 24 months ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
12
votes
20
replies
14k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 13 months ago by
Ram
43k • written 4.9 years ago by
jared.andrews07
★ 16k
90
votes
19
replies
32k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
47
votes
19
replies
13k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 15 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
42
votes
19
replies
7.9k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Daniel Standage
4.1k
8
votes
19
replies
13k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 13 months ago by
Ram
43k • written 9.4 years ago by
Lesley Sitter
▴ 600
53
votes
19
replies
44k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 14 months ago by
Ram
43k • written 12.0 years ago by
Sukhi Singh
11k
23
votes
19
replies
6.9k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 12 months ago by
Ram
43k • written 7.6 years ago by
chen
★ 2.5k
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 12 months ago by
GenoMax
141k • written 10.4 years ago by
Obi Griffith
20k
26
votes
17
replies
7.7k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 19 months ago by
Ram
43k • written 9.7 years ago by
Ian
6.0k
12
votes
17
replies
3.0k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Istvan Albert
100k
8
votes
17
replies
3.2k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
alignment
next-gen-sequencing
RNA-seq
updated 20 months ago by
Ram
43k • written 8.6 years ago by
elia.brodsky
▴ 340
99
votes
16
replies
34k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 13 months ago by
Ram
43k • written 7.7 years ago by
Jean-Karim Heriche
27k
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
42
votes
16
replies
24k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 21 months ago by
Ram
43k • written 8.6 years ago by
Chirag Nepal
★ 2.4k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 6 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
34
votes
15
replies
6.5k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 13 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
26
votes
15
replies
8.9k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Medhat
9.7k
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 5.6 years ago by
finswimmer
16k
411 results • Page
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Recent Votes
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
Answer: Discrepancy between Log2(x) and Log2(x+1) regarding Log2FC
Answer: Verify if all the components of a pathway are present in a genomes
Answer: p-value in CIBERSORT
Answer: Can I have multiple active GDC download tokens?
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elcortegano
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i.sudbery
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Recent Replies
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems
by
Ram
43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
Comment: Post-imputation plot
by
kl
▴ 10
All of them are G/C and A/T variants Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
Nafi
• 0
Thank you for the reply I have 16 gb of RAM then I can give a try then.
Comment: Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
by
i.sudbery
19k
Can you give more details of the data you are planning to use. What is the different studies, what are the comparisons you want to make.
Comment: p-value in CIBERSORT
by
michelafrancesconi9
▴ 20
Thank you so much!!
Comment: POSSUM not working due to incompatible pssm file
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Telescope issue
by
GenoMax
141k
Looks like there is a tab missing between the sequence and the quality string.
Comment: Post-imputation plot
by
LChart
3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
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