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3,342 results • Page
1 of 67
Sort: Views
Rank
Views
Votes
Replies
64
votes
3
replies
268k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 17 days ago by
Ram
38k • written 8.8 years ago by
Whoknows
▴ 960
729
votes
161
replies
108k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
97k
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 19 days ago by
Genetics
▴ 20 • written 10.8 years ago by
GouthamAtla
12k
274
votes
33
replies
92k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 22 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
118
votes
53
replies
87k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 4 days ago by
Raag
• 0 • written 8.8 years ago by
kay
▴ 330
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 10 days ago by
4galaxy77
2.6k • written 10.8 years ago by
Rubal7
▴ 820
24
votes
10
replies
58k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 14 days ago by
Ram
38k • written 2.0 years ago by
Nitin Narwade
★ 1.3k
45
votes
14
replies
58k
views
10 follow
Tutorial:
Using R in Conda
R
updated 9 days ago by
Ram
38k • written 2.7 years ago by
rohitsatyam102
▴ 690
146
votes
35
replies
58k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 28 days ago by
Ram
38k • written 10.3 years ago by
vijay
★ 1.6k
79
votes
2
replies
53k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 24 days ago by
Ram
38k • written 9.7 years ago by
Eric Normandeau
11k
1
vote
6
replies
52k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 6 days ago by
Ram
38k • written 6.2 years ago by
IOM
• 0
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 27 days ago by
Ram
38k • written 9.9 years ago by
Cyriac Kandoth
5.9k
26
votes
21
replies
50k
views
9 follow
How To Convert List Of Entrez Ids Into Gene Name
r
genomics
entrez
updated 27 days ago by
Ram
38k • written 9.9 years ago by
grosy
▴ 90
48
votes
19
replies
49k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle
perl
samtools
updated 15 days ago by
Ram
38k • written 12.5 years ago by
Stew
★ 1.4k
66
votes
18
replies
46k
views
16 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
tools
updated 10 days ago by
Muhammad
• 0 • written 10.1 years ago by
14134125465346445
★ 3.6k
144
votes
68
replies
43k
views
18 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 9 days ago by
Ram
38k • written 5.3 years ago by
Kevin Blighe
84k
26
votes
9
replies
40k
views
How Logfc Value Is Calculated In Edger?
edger
r
RNA-seq
updated 23 days ago by
Ram
38k • written 9.5 years ago by
nbvasani
▴ 240
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 9 days ago by
Ram
38k • written 4.7 years ago by
ATpoint
70k
60
votes
52
replies
39k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 9 days ago by
Ram
38k • written 6.5 years ago by
steve
★ 3.3k
206
votes
58
replies
38k
views
31 follow
Forum:
Will Python Take The Place Of R?
r
statistics
python
biopython
updated 26 days ago by
Ram
38k • written 9.8 years ago by
Medhat
9.5k
20
votes
12
replies
37k
views
7 follow
Forum:
When To Use Sed Awk Over Perl Or Python
perl
python
awk
updated 21 days ago by
Ram
38k • written 9.2 years ago by
Medhat
9.5k
115
votes
35
replies
36k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
Forum
updated 13 days ago by
e.r.zakiev
▴ 30 • written 5.8 years ago by
ropolocan
▴ 760
58
votes
25
replies
36k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 6 days ago by
Ram
38k • written 6.7 years ago by
Shicheng Guo
★ 9.3k
41
votes
17
replies
35k
views
15 follow
Forum:
List Of Genome Sequencing Centers/Institutes
genomics
institutes
updated 27 days ago by
Ram
38k • written 10.1 years ago by
Malachi Griffith
19k
92
votes
105
replies
34k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 9 days ago by
Ram
38k • written 4.6 years ago by
Kevin Blighe
84k
13
votes
3
replies
33k
views
Drawing venn diagram in R
ChIP-Seq
venn-diagram
updated 2 days ago by
Ram
38k • written 7.9 years ago by
Rashedul Islam
▴ 450
118
votes
26
replies
32k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 13 days ago by
e.r.zakiev
▴ 30 • written 7.8 years ago by
mhockin
▴ 610
21
votes
3
replies
31k
views
Forum:
Did You Know That Researchgate Is Spamming Your Colleagues (Perhaps Without Your Explicit Consent)?
researchgate
updated 28 days ago by
Ram
38k • written 10.1 years ago by
Obi Griffith
20k
27
votes
16
replies
31k
views
16 follow
How Do I Convert Fa Files To Bed Format?
fasta
bed
updated 7 days ago by
shelkmike
▴ 920 • written 11.3 years ago by
Keziah
▴ 70
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 29 days ago by
Ram
38k • written 10.5 years ago by
Istvan Albert
97k
251
votes
36
replies
30k
views
27 follow
Forum:
How Do You Manage Your Files & Directories For Your Projects ?
project-management
file-management
updated 4 hours ago by
Ram
38k • written 12.9 years ago by
Pierre Lindenbaum
153k
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 22 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 9 days ago by
Ram
38k • written 6.6 years ago by
Jean-Karim Heriche
26k
65
votes
17
replies
30k
views
12 follow
Transform a GTF file into a data frame in R
R
RNA-Seq
GTF
updated 23 days ago by
Ram
38k • written 5.5 years ago by
biomagician
▴ 350
130
votes
123
replies
28k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 1 day ago by
krushnach80
★ 1.1k • written 4.4 years ago by
Kevin Blighe
84k
126
votes
44
replies
27k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 14 days ago by
Ram
38k • written 6.5 years ago by
Lars
▴ 970
50
votes
14
replies
27k
views
8 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 23 days ago by
Ram
38k • written 9.7 years ago by
user
▴ 930
100
votes
36
replies
27k
views
33 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 1 day ago by
Simon
▴ 20 • written 9.4 years ago by
14134125465346445
★ 3.6k
31
votes
12
replies
26k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 23 days ago by
Ram
38k • written 9.4 years ago by
Istvan Albert
97k
57
votes
19
replies
26k
views
6 follow
Forum:
Attention: Bowtie2 And Multiple Hits
next-gen
bowtie
mapping
updated 28 days ago by
Ram
38k • written 10.4 years ago by
David Langenberger
9.9k
63
votes
27
replies
26k
views
18 follow
Data Too Big To Be Stored In Memory: Common Options
python
updated 28 days ago by
Ram
38k • written 10.3 years ago by
Click downvote
▴ 720
45
votes
15
replies
25k
views
15 follow
How To Do Normalization Of Two Chip-Seq Data?
chip-seq
updated 23 days ago by
baijiangshan9726
• 0 • written 11.0 years ago by
yatung
▴ 200
25
votes
13
replies
25k
views
8 follow
Bowtie2 parameters for best alignment
alignment
Assembly
genome
SNP
updated 3 days ago by
Medhat
9.5k • written 8.8 years ago by
cvu
▴ 180
67
votes
6
replies
24k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 29 days ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
97k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 20 days ago by
Ram
38k • written 9.1 years ago by
Istvan Albert
97k
6
votes
22
replies
24k
views
12 follow
CluserProfiler message "No gene can be mapped"
R
updated 1 day ago by
joe555
• 0 • written 5.0 years ago by
ARich
▴ 130
31
votes
9
replies
24k
views
11 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 9 days ago by
Ram
38k • written 2.6 years ago by
lavinia.gordon
▴ 140
19
votes
5
replies
23k
views
Hypergeometric Test On Gene Set
r
statistics
updated 21 days ago by
Ram
38k • written 9.2 years ago by
ChIP
▴ 600
151
votes
39
replies
22k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
updated 28 days ago by
Ram
38k • written 10.2 years ago by
Martin A Hansen
3.0k
32
votes
14
replies
22k
views
15 follow
Where can I find public Single Cell RNA-seq data?
RNA-Seq
sequencing
updated 29 days ago by
Aqsa
• 0 • written 6.6 years ago by
309772486
▴ 140
3,342 results • Page
1 of 67
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Comment: bioinformatics problems solved by graphs data structure
Comment: bioinformatics problems solved by graphs data structure
Answer: How to analize multiple letters codes in COG IDs?
Answer: PCA in gene expression
Answer: PCA in gene expression
Comment: Enrichment analysis based on kegg for zebrafish
Question on number of possible alignments
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Comment: How to analize multiple letters codes in COG IDs?
by
Constanza
• 0
Thanks for answering so fast, it was very helpful. I shouldn't pay much attention to if COGs are separated by a comma or not then. As long…
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts
by
lieven.sterck
14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that ID…
Answer: How to analize multiple letters codes in COG IDs?
by
Mensur Dlakic
★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
by
Pierre Lindenbaum
153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error
by
Medha
• 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error
by
jared.andrews07
★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error
by
Medha
• 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE
by
Mensur Dlakic
★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis
by
Chris
▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
by
jv
★ 1.0k
`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis
by
jv
★ 1.0k
run `union` on the data frames
Comment: PCA in gene expression
by
ali
• 0
Thanks for your attention. yes I know that we should not omit the samples, I just worry about noises on my differential expression and some…
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