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107,898 results • Page
1 of 2158
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
279k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 5 months ago by
Ram
37k • written 13.3 years ago by
Renee
▴ 620
63
votes
3
replies
263k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
expression
gene
Tutorial
RNA-Seq
protein
updated 16 months ago by
Ram
37k • written 8.7 years ago by
Whoknows
▴ 950
267
votes
29
replies
246k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 weeks ago by
Ram
37k • written 10.3 years ago by
sohadb1357
▴ 610
318
votes
90
replies
210k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 4 months ago by
Ram
37k • written 12.0 years ago by
Biomed
4.8k
43
votes
24
replies
191k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 10 months ago by
matthew.pace
▴ 40 • written 9.2 years ago by
Arpitha Hebbar
▴ 210
59
votes
12
replies
180k
views
7 follow
How To Deal With Duplicate Row Names Error In R
r
updated 13 months ago by
Ram
37k • written 10.0 years ago by
Diana
▴ 900
12
votes
6
replies
175k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 2.4 years ago by
zx8754
11k • written 5.0 years ago by
hassanlou110
▴ 40
151
votes
42
replies
173k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 8 months ago by
Ram
37k • written 10.9 years ago by
Obi Griffith
20k
118
votes
31
replies
170k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta
parsing
python
updated 16 months ago by
GenoMax
125k • written 12.8 years ago by
Eric Normandeau
11k
124
votes
19
replies
169k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 21 months ago by
kajumi
• 0 • written 10.6 years ago by
shiy05
▴ 350
141
votes
14
replies
162k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 3.2 years ago by
Renesh
★ 2.1k • written 12.8 years ago by
Pierre Lindenbaum
152k
273
votes
39
replies
161k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 9 months ago by
Ram
37k • written 8.4 years ago by
Obi Griffith
20k
188
votes
21
replies
161k
views
11 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 10 weeks ago by
Istvan Albert
96k • written 12.2 years ago by
Andrea_Bio
★ 2.8k
122
votes
11
replies
155k
views
11 follow
How Can I Convert Bam To Sam?
next-gen
sequencing
bam
sam
conversion
updated 17 months ago by
t.montserrat.ayuso
• 0 • written 12.6 years ago by
Biomed
4.8k
131
votes
18
replies
152k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 7 weeks ago by
katieostrouchov
▴ 20 • written 9.1 years ago by
timjoncooper
▴ 310
158
votes
8
replies
146k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 6 months ago by
Ram
37k • written 10.1 years ago by
lyz10302012
▴ 430
358
votes
79
replies
135k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 10 weeks ago by
Ram
37k • written 10.0 years ago by
ole.tange
★ 4.3k
220
votes
38
replies
132k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 7 weeks ago by
harelarik
▴ 90 • written 9.9 years ago by
Malachi Griffith
19k
10
votes
4
replies
132k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 11.6 years ago by
Stefano Berri
4.3k • written 11.6 years ago by
Don
▴ 20
89
votes
38
replies
124k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 4 months ago by
Wang Cong
▴ 10 • written 10.6 years ago by
abi
▴ 370
140
votes
30
replies
124k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 4 months ago by
Ram
37k • written 11.0 years ago by
Anima Mundi
★ 2.9k
129
votes
32
replies
121k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 10 months ago by
Ram
37k • written 11.9 years ago by
Gon
▴ 530
23
votes
9
replies
120k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 6.5 years ago by
Vasei
▴ 30 • written 7.8 years ago by
juan.rosas1
▴ 70
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics
r
updated 7 months ago by
Ram
37k • written 11.0 years ago by
Diana
▴ 900
116
votes
25
replies
117k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 6.0 years ago by
Hajk-Georg Drost
▴ 160 • written 12.5 years ago by
Biomed
4.8k
13
votes
8
replies
115k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 4 months ago by
Ram
37k • written 11.2 years ago by
Zhshqzyc
▴ 490
160
votes
52
replies
115k
views
28 follow
Fastq Convert To Fasta
perl
9.2 years ago by
biolab
★ 1.4k
3
votes
3
replies
112k
views
Find mismatch in two columns in a data frame in R
R
updated 6.9 years ago by
dan.shea
▴ 10 • written 6.9 years ago by
dirranrak
▴ 20
46
votes
10
replies
111k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 7 weeks ago by
Ram
37k • written 9.8 years ago by
biorepine
★ 1.5k
115
votes
21
replies
111k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 10.9 years ago by
Aditya Joshi
▴ 30 • written 11.2 years ago by
Niek De Klein
★ 2.6k
97
votes
9
replies
111k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 9 months ago by
henry-keen
▴ 40 • written 9.4 years ago by
newDNASeqer
▴ 750
91
votes
10
replies
105k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 10.8 years ago by
Guangchuang Yu
★ 2.6k • written 10.8 years ago by
Wayne
★ 1.0k
28
votes
8
replies
105k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 11.9 years ago by
User 5402
▴ 210
715
votes
159
replies
104k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
1.5k • written 6.2 years ago by
Istvan Albert
96k
117
votes
7
replies
104k
views
Bam And Indexed Bam Files
bam
index
11.1 years ago by
Sahel
▴ 260
63
votes
16
replies
102k
views
11 follow
from .BAM to .BAI using samtools
sequencing
samtools
next-gen
updated 12 months ago by
Ram
37k • written 8.3 years ago by
Kizuna
▴ 860
118
votes
15
replies
101k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.0 years ago by
Mona Mohamed
• 0 • written 12.2 years ago by
Terence
▴ 210
31
votes
8
replies
96k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 12.1 years ago by
Hazel
• 0 • written 12.7 years ago by
Hazel
▴ 70
98
votes
14
replies
95k
views
14 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 10 months ago by
Juke34
7.5k • written 10.7 years ago by
GouthamAtla
12k
72
votes
25
replies
94k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 7 months ago by
Ram
37k • written 7.8 years ago by
Chenglin
▴ 250
93
votes
31
replies
94k
views
20 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 11 months ago by
Dan
▴ 60 • written 10.7 years ago by
GPR
▴ 380
59
votes
9
replies
92k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
RNA-Seq
Blog
gene
expression
17 months ago by
Renesh
★ 2.1k
274
votes
33
replies
90k
views
24 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 12 months ago by
tshtatland
▴ 100 • written 9.3 years ago by
Obi Griffith
20k
173
votes
30
replies
87k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 12 months ago by
Ram
37k • written 11.8 years ago by
Ct586
▴ 610
97
votes
19
replies
86k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 5 months ago by
Ram
37k • written 13.0 years ago by
Giovanni M Dall'Olio
27k
115
votes
52
replies
85k
views
21 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 2 days ago by
Ram
37k • written 8.6 years ago by
kay
▴ 320
43
votes
15
replies
84k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna
edger
r
counts
updated 8.2 years ago by
seidel
10k • written 11.8 years ago by
Jason
▴ 910
70
votes
16
replies
84k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 10 months ago by
Pierre Lindenbaum
152k • written 11.4 years ago by
Sakti
▴ 510
39
votes
8
replies
84k
views
samtools sorting and indexing
samtools
index
sort
updated 3.0 years ago by
onestop_data
▴ 320 • written 5.6 years ago by
ggman
▴ 80
166
votes
41
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 3 days ago by
Onur
• 0 • written 11.6 years ago by
Palu
▴ 240
107,898 results • Page
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Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
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Answer: What is the difference between a Read and a Fragment in RNA-seq?
lncRNA analysis tutorial
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
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Recent Replies
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
• 0
This does not work. I called for the gene "Cd8a" for instance for the mouse genome and it says "Gene not found" even though it should appea…
Comment: How to extract the list of genes from TCGA CNV data
by
Kevin Blighe
84k
Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
Comment: RNASeq differential expression masked by pathways disregulation
by
ATpoint
68k
If this is the case then you cannot correct for anything as this effect is nested with center.
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
That error message is very descriptive. Could you also add the line 997531?
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴ 110
Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
Comment: Is the heterozygosity flag (--het) in vcftools calculate observed and expected h
by
dr.fakharunnisa
• 0
Hello #gubrins Have you found the answer
Comment: CoveragePlot in Signac from MACS2 Object
by
seidel
10k
The `object` will the the Seurat object you're working with, because that contains the data that will be plotted (Tn5 insertion events per …
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date
by
GenoMax
125k
Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong. $ esearch -db nu…
Comment: Faking hh-suite workflow / alignment output
by
Mensur Dlakic
★ 22k
Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
Answer: Manual Polygenic Risk Score calculation
by
Sam
★ 4.6k
Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
Comment: Single sample GSEA analysis
by
tujuchuanli
▴ 100
Hi jv, Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
by
Jiyao Wang
▴ 290
You can also try out [iCn3D](https://structure.ncbi.nlm.nih.gov/icn3d). After you load your custom PDB via the menu "File > Open File > PDB…
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
• 0
What is 'peaks' entered as?... The input is: CoveragePlot( object = pbmc, region = "CD8A", ranges = peaks, …
Comment: Faking hh-suite workflow / alignment output
by
Nick
▴ 40
I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
Comment: CoveragePlot in Signac from MACS2 Object
by
seidel
10k
Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
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