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90,475 results • Page
1 of 1810
Sort: Views
Rank
Views
Votes
Replies
222
votes
38
replies
263k
views
31 follow
Gene Id Conversion Tool
mapping
conversion
updated 14 months ago by
tamerg
▴ 90 • written 11.5 years ago by
Renee
▴ 620
49
votes
3
replies
203k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
RNA-Seq
expression
gene
protein
Tutorial
updated 3.8 years ago by
FatihSarigol
▴ 220 • written 6.9 years ago by
Whoknows
▴ 860
225
votes
29
replies
187k
views
23 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 days ago by
srhhaines9
• 0 • written 8.4 years ago by
sohadb1357
▴ 520
290
votes
77
replies
171k
views
49 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 2.7 years ago by
WouterDeCoster
45k • written 10.2 years ago by
Biomed
4.7k
145
votes
42
replies
159k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 21 months ago by
sansritisinha
• 0 • written 9.1 years ago by
Obi Griffith
19k
42
votes
23
replies
156k
views
23 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 11 months ago by
brianpenghe
▴ 50 • written 7.4 years ago by
Arpitha Hebbar
▴ 200
115
votes
18
replies
151k
views
11 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 12 months ago by
ciro.santilli
▴ 20 • written 8.8 years ago by
shiy05
▴ 330
134
votes
14
replies
146k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 16 months ago by
Renesh
★ 2.0k • written 11.0 years ago by
Pierre Lindenbaum
135k
51
votes
11
replies
139k
views
6 follow
How To Deal With Duplicate Row Names Error In R
r
updated 8.2 years ago by
Michael Dondrup
48k • written 8.2 years ago by
Diana
▴ 860
145
votes
19
replies
137k
views
9 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 10.2 years ago by
Neilfws
49k • written 10.4 years ago by
Andrea_Bio
★ 2.6k
110
votes
9
replies
130k
views
8 follow
How Can I Convert Bam To Sam?
next-gen
sequencing
bam
sam
conversion
updated 7.4 years ago by
Chris Miller
21k • written 10.8 years ago by
Biomed
4.7k
250
votes
39
replies
124k
views
27 follow
Tutorial:
How to download raw sequence data from GEO/SRA
GEO
SRA
fastq
bam
download
Tutorial
updated 2 days ago by
cicindel
▴ 70 • written 6.6 years ago by
Obi Griffith
19k
341
votes
80
replies
123k
views
32 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
tools
parallel
next-gen
ngs
Tool
4 months ago by
ole.tange
★ 4.0k
110
votes
19
replies
121k
views
14 follow
Blast - Formatting Output
blast
format
output
updated 6 months ago by
apekshasharma7777
• 0 • written 7.3 years ago by
timjoncooper
▴ 240
108
votes
28
replies
118k
views
15 follow
Correct Way To Parse A Fasta File In Python
fasta
parsing
python
updated 2.6 years ago by
Ram
32k • written 11.0 years ago by
Eric Normandeau
11k
10
votes
4
replies
116k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 9.8 years ago by
Stefano Berri
4.2k • written 9.8 years ago by
Don
▴ 20
198
votes
30
replies
112k
views
22 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 3 months ago by
zlbio12
• 0 • written 8.1 years ago by
Malachi Griffith
18k
26
votes
10
replies
109k
views
Calculating P-Values From Z-Scores
statistics
r
updated 2.5 years ago by
Kevin Blighe
72k • written 9.2 years ago by
Diana
▴ 860
22
votes
9
replies
109k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 4.7 years ago by
Vasei
▴ 30 • written 6.0 years ago by
juan.rosas1
▴ 70
127
votes
32
replies
108k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 2.0 years ago by
malina
• 0 • written 10.1 years ago by
Gon
▴ 520
110
votes
25
replies
108k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 4.2 years ago by
Hajk-Georg Drost
▴ 160 • written 10.7 years ago by
Biomed
4.7k
115
votes
21
replies
106k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 9.1 years ago by
Aditya Joshi
▴ 30 • written 9.4 years ago by
Niek De Klein
★ 2.5k
28
votes
8
replies
102k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 10.1 years ago by
User 5402
▴ 210
88
votes
10
replies
101k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 9.0 years ago by
Guangchuang Yu
★ 2.4k • written 9.0 years ago by
Wayne
★ 1.0k
124
votes
28
replies
99k
views
23 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 3.5 years ago by
Joe
19k • written 9.2 years ago by
Anima Mundi
★ 2.8k
46
votes
10
replies
98k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 16 months ago by
Renesh
★ 2.0k • written 8.0 years ago by
biorepine
★ 1.5k
3
votes
3
replies
98k
views
Find mismatch in two columns in a data frame in R
R
updated 5.1 years ago by
dan.shea
▴ 10 • written 5.1 years ago by
dirranrak
▴ 20
118
votes
8
replies
97k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 2.6 years ago by
zx8754
10k • written 8.3 years ago by
lyz10302012
▴ 360
145
votes
52
replies
96k
views
28 follow
Fastq Convert To Fasta
perl
updated 17 months ago by
brianpenghe
▴ 50 • written 7.4 years ago by
biolab
★ 1.3k
115
votes
15
replies
95k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 10.2 years ago by
Mona Mohamed
• 0 • written 10.4 years ago by
Terence
▴ 190
31
votes
8
replies
94k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 10.2 years ago by
Hazel
• 0 • written 10.9 years ago by
Hazel
▴ 70
12
votes
8
replies
93k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5.2 years ago by
BioApps
▴ 780 • written 9.4 years ago by
Zhshqzyc
▴ 490
84
votes
9
replies
86k
views
9 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 7.6 years ago by
Pierre Lindenbaum
135k • written 7.6 years ago by
newDNASeqer
▴ 710
10
votes
6
replies
84k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 7 months ago by
zx8754
10k • written 3.2 years ago by
hassanlou110
▴ 30
102
votes
7
replies
84k
views
Bam And Indexed Bam Files
bam
index
9.3 years ago by
Sahel
▴ 220
72
votes
28
replies
84k
views
15 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 12 months ago by
gubrins
▴ 70 • written 8.8 years ago by
abi
▴ 330
166
votes
30
replies
80k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 6.5 years ago by
Prakki Rama
★ 2.4k • written 10.0 years ago by
Ct586
▴ 560
92
votes
19
replies
76k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 4.9 years ago by
jayanthisreejith7
▴ 10 • written 11.2 years ago by
Giovanni M Dall'Olio
27k
43
votes
15
replies
72k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna
edger
r
counts
updated 6.4 years ago by
seidel
7.6k • written 10.0 years ago by
Jason
▴ 900
98
votes
16
replies
72k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq
coverage
6.4 years ago by
Obi Griffith
19k
109
votes
8
replies
71k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi
ucsc
grch38
hg38
updated 6.5 years ago by
Denise CS
★ 5.1k • written 6.6 years ago by
pwg46
▴ 450
54
votes
14
replies
71k
views
10 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 4.7 years ago by
brent_wilson
▴ 110 • written 9.6 years ago by
Sakti
▴ 440
181
votes
43
replies
71k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 3.4 years ago by
bernatgel
★ 2.9k • written 11.1 years ago by
Yuri
★ 1.6k
82
votes
12
replies
70k
views
12 follow
Convertion Of Gff3 To Gtf
gff
gtf
updated 13 months ago by
Juke34
★ 5.3k • written 8.9 years ago by
GouthamAtla
11k
57
votes
11
replies
70k
views
8 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
RNA-Seq
gene expression
Blog
2.7 years ago by
Renesh
★ 2.0k
92
votes
43
replies
68k
views
27 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 19 months ago by
romain.lannes
▴ 80 • written 8.7 years ago by
Mchimich
▴ 280
69
votes
18
replies
68k
views
11 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 5.9 years ago by
Reece
▴ 310 • written 10.4 years ago by
Unode
▴ 180
76
votes
24
replies
68k
views
18 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 10 weeks ago by
opplatek
▴ 110 • written 8.9 years ago by
GPR
▴ 330
224
votes
175
replies
68k
views
72 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 21 days ago by
Ram
32k • written 5.7 years ago by
TriS
★ 4.3k
228
votes
32
replies
67k
views
22 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 8 weeks ago by
ashotmarg2004
▴ 10 • written 7.5 years ago by
Obi Griffith
19k
90,475 results • Page
1 of 1810
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Answer: Hunting invisible characters?
Comment: Genotype Data in PLINK
Comment: Hunting invisible characters?
Comment: Hunting invisible characters?
Comment: A simple tutorial for a complex ComplexHeatmap
Comment: A simple tutorial for a complex ComplexHeatmap
Comment: A simple tutorial for a complex ComplexHeatmap
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Answer: GSEA for RNA_seq dataset
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Using all genes with signed P-value to rank genes, where the sign is from LogFC. and `GSEAPreranked` module in GSEA. ref: [Gene Ranki…
Comment: How can I Extract Transposable element from a new genome assembly?
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if you can transform the bed to gff (galaxy has tools for that), you could also use liftoff which wraps all of this in a pipeline https://g…
Comment: A simple tutorial for a complex ComplexHeatmap
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Great! Thank you ATpoint
Comment: Hunting invisible characters?
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7.6k
Another way to see hidden characters is to pipe them through octal dump: `cat infile | od -c` this will print out hidden characters, newlin…
Comment: How can I Extract Transposable element from a new genome assembly?
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Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
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It is going to take as long as it takes. You need to be patient and wait until the prompt returns. Based on speed of your CPU/disk things c…
Comment: Hunting invisible characters?
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GenoMax
99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
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I'm not sure about three things: What does -M and -O do exactly that could benefit in my case? Why should I specify -t if I don't necessa…
Comment: Hunting invisible characters?
by
geneticatt
▴ 120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters?
by
Mensur Dlakic
★ 10k
You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing: dos2unix i5R.txt If an error pops …
Comment: RNA seq analysis; two samples
by
Ram
32k
Please do not delete posts that have comments/answers.
Comment: ICE normalization using JuicerTools
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sckinta
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Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
Comment: How to verify putative miRNA
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Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well. [1]: https://j…
Comment: R - A bioinformatic analysis programming language for NGS
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Because this is a plain copy-paste from the novogene page, it has numbers (pointers to specific references that the source has), but not th…
Comment: X amino acid in ensembl
by
Mensur Dlakic
★ 10k
This is correct. `X` means any amino acid. Most substitution matrices apply identical penalty (`-1`) when any amino-acid is aligned with X …
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