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410 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 8.7 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
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 11 days ago by
psb7
▴ 20 • written 5.6 years ago by
Kevin Blighe
87k
76
votes
70
replies
19k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 13 months ago by
Ram
43k • written 6.2 years 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 7 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
81k
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 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
196
votes
44
replies
71k
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 9.6 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
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 10 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
147
votes
34
replies
54k
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
298
votes
33
replies
108k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 13 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
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
8.5k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 5 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
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 22 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
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
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
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
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
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
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
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 7.7 years ago by
Shicheng Guo
★ 9.4k
139
votes
25
replies
83k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 2.0 years ago by
Ram
43k • written 12.0 years ago by
Ying W
★ 4.2k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 2 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
93
votes
23
replies
91k
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 5.7 years ago by
otwtgin2010
▴ 610
142
votes
21
replies
30k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 23 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
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
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 13 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
42
votes
19
replies
7.8k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Daniel Standage
4.1k
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
53
votes
19
replies
43k
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
6.8k
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
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
2.9k
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 8.8 years ago by
Istvan Albert
100k
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
8
votes
17
replies
3.1k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
alignment
next-gen-sequencing
RNA-seq
updated 19 months ago by
Ram
43k • written 8.5 years ago by
elia.brodsky
▴ 340
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
99
votes
16
replies
33k
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
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 4 weeks ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
42
votes
16
replies
23k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Chirag Nepal
★ 2.4k
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 4.8 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 5.5 years ago by
finswimmer
16k
410 results • Page
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Answer: Ubuntu storage space is decreasing automatically
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
Answer: RNA seq differential expression analysis
Answer: MEGA Analysis Issue on High-Performance Computer
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Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
by
Gordon Smyth
★ 7.0k
Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
Comment: Free/open source 23andme-like analysis
by
swbarnes2
14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
swbarnes2
14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
ATpoint
81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file
by
swbarnes2
14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
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Matthias Zepper
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It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
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